From 94ea26298514d4e011a60d6c29ad35fd4ba5fd3a Mon Sep 17 00:00:00 2001 From: nkrumm Date: Fri, 21 Sep 2018 10:25:19 -0700 Subject: [PATCH 01/34] Python3 fixes: - fix chrom_sort function, which compared strings to ints - s/xrange/range - fix some string/bytestring handling - remove tuple destructoring --- BPMReader.py | 2 +- GenotypeFormat.py | 2 +- IlluminaBeadArrayFiles.py | 36 ++++++++++++++++++------------------ LocusEntryFactory.py | 2 +- gtc_to_vcf.py | 7 ++++++- tests/test_class.py | 2 +- 6 files changed, 28 insertions(+), 23 deletions(-) diff --git a/BPMReader.py b/BPMReader.py index 110261a..1aeb23c 100644 --- a/BPMReader.py +++ b/BPMReader.py @@ -35,7 +35,7 @@ def get_bpm_records(self): BPMRecord: Next BPMRecord in the file """ bpm = self._bpm - for idx in xrange(len(bpm.addresses)): + for idx in range(len(bpm.addresses)): yield BPMRecord(bpm.names[idx], bpm.addresses[idx], None, bpm.chroms[idx], bpm.map_infos[idx], bpm.snps[idx], bpm.ref_strands[idx], bpm.assay_types[idx], None, None, None, None, idx, self._logger) class ManifestFilter(object): diff --git a/GenotypeFormat.py b/GenotypeFormat.py index a94b4fa..6e45b77 100644 --- a/GenotypeFormat.py +++ b/GenotypeFormat.py @@ -221,7 +221,7 @@ def _filter_inconsistent_genotypes(self, possible_genotypes): length 2 where each string is a nucleotide on the plus strand """ idx2inconsistent = [False] * len(possible_genotypes) - for idx in xrange(len(possible_genotypes)): + for idx in range(len(possible_genotypes)): for record in self._bpm_records: if self._record_inconsistent_with_genotype(record, possible_genotypes[idx]): idx2inconsistent[idx] = True diff --git a/IlluminaBeadArrayFiles.py b/IlluminaBeadArrayFiles.py index b1bb8e6..0e5af90 100644 --- a/IlluminaBeadArrayFiles.py +++ b/IlluminaBeadArrayFiles.py @@ -139,7 +139,7 @@ def __init__(self, filename, ignore_version = False, check_write_complete = True self.filename = filename with open(self.filename, "rb") as gtc_handle: identifier = gtc_handle.read(3) - if identifier != "gtc": + if identifier != b'gtc': raise Exception("GTC format error: bad format identifier") self.version = read_byte(gtc_handle) if self.version not in GenotypeCalls.supported_version and not ignore_version: @@ -151,7 +151,7 @@ def __init__(self, filename, ignore_version = False, check_write_complete = True # to the lookup # self.toc_table = {} - for toc_idx in xrange(number_toc_entries): + for toc_idx in range(number_toc_entries): (id, offset) = struct.unpack("= 100: raise Exception("Manifest format error: read invalid normalization ID") @@ -741,7 +741,7 @@ def __parse_file(self, manifest_file): self.map_infos = [0] * self.num_loci self.ref_strands = [RefStrand.Unknown] * self.num_loci self.source_strands = [SourceStrand.Unknown] * self.num_loci - for idx in xrange(self.num_loci): + for idx in range(self.num_loci): locus_entry = LocusEntry(manifest_handle) self.assay_types[name_lookup[locus_entry.name]] = locus_entry.assay_type self.addresses[name_lookup[locus_entry.name]] = locus_entry.address_a @@ -755,12 +755,12 @@ def __parse_file(self, manifest_file): raise Exception("Manifest format error: read invalid number of assay entries") all_norm_ids = set() - for locus_idx in xrange(self.num_loci): + for locus_idx in range(self.num_loci): self.normalization_ids[locus_idx] += 100 * self.assay_types[locus_idx] all_norm_ids.add(self.normalization_ids[locus_idx]) sorted_norm_ids = sorted(all_norm_ids) lookup_dictionary = {} - for idx in xrange(len(sorted_norm_ids)): + for idx in range(len(sorted_norm_ids)): lookup_dictionary[sorted_norm_ids[idx]] = idx self.normalization_lookups = [lookup_dictionary[normalization_id] for normalization_id in self.normalization_ids] @@ -913,21 +913,21 @@ def __parse_locus_version_6(self,handle): self.ilmn_id = read_string(handle) self.source_strand = SourceStrand.from_string(self.ilmn_id.split("_")[-2]) self.name = read_string(handle) - for idx in xrange(3): + for idx in range(3): read_string(handle) handle.read(4) - for idx in xrange(2): + for idx in range(2): read_string(handle) self.snp = read_string(handle) self.chrom = read_string(handle) - for idx in xrange(2): + for idx in range(2): read_string(handle) self.map_info = int(read_string(handle)) - for idx in xrange(2): + for idx in range(2): read_string(handle) self.address_a = read_int(handle) self.address_b = read_int(handle) - for idx in xrange(7): + for idx in range(7): read_string(handle) handle.read(3) self.assay_type = read_byte(handle) @@ -1038,7 +1038,7 @@ def read_string(handle): if len(result) < total_length: raise Exception("Failed to read complete string") else: - return result + return result.decode() def read_scanner_data(handle): """Helper function to parse ScannerData object from file handle. diff --git a/LocusEntryFactory.py b/LocusEntryFactory.py index 7592c47..1e23f0e 100644 --- a/LocusEntryFactory.py +++ b/LocusEntryFactory.py @@ -55,7 +55,7 @@ def _group_bpm_records(self, bpm_records): position = (record.chromosome, record.pos, (record.get_indel_source_sequences(RefStrand.Plus)[1], record.is_deletion) if record.is_indel() else None) position2record.setdefault(position, []).append(record) - for _, value in position2record.iteritems(): + for _, value in position2record.items(): if len(value) > 1 and self._unsquash_duplicates: alleles = set() for bpm_record in value: diff --git a/gtc_to_vcf.py b/gtc_to_vcf.py index a36382d..14502b9 100755 --- a/gtc_to_vcf.py +++ b/gtc_to_vcf.py @@ -72,11 +72,16 @@ def verify_inputs(args): return errors + +CHROM_DICT = { + "X": 23, "Y": 24, "MT": 25 +} + def chrom_sort(chrom_string): """ Convert input chromosome string to appropriate type to ensure native sort functions sorts chromosomes in order 1-22,X,Y,MT """ - return int(chrom_string) if str(chrom_string).isdigit() else chrom_string.lower() + return int(chrom_string) if str(chrom_string).isdigit() else CHROM_DICT.get(chrom_string, 26) def get_sample_name(gtc, gtc_file): sample_name = gtc.get_sample_name() diff --git a/tests/test_class.py b/tests/test_class.py index c022759..fe5c323 100644 --- a/tests/test_class.py +++ b/tests/test_class.py @@ -97,7 +97,7 @@ def test_source_sequence_split(self): class TestCombinedGenotypes(unittest.TestCase): def check_genotype(self, data, expected_genotype): records = [datum[0] for datum in data] - for idx in xrange(len(records)): + for idx in range(len(records)): records[idx].index_num = idx genotypes = [datum[1] for datum in data] combiner = RecordCombiner(records, genotypes, "") From 91686b52caa2f0305c39251fbb42025fb2b099b3 Mon Sep 17 00:00:00 2001 From: KelleyRyanM Date: Tue, 27 Nov 2018 20:15:45 -0800 Subject: [PATCH 02/34] Update VcfRecordFactory.py --- VcfRecordFactory.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VcfRecordFactory.py b/VcfRecordFactory.py index 3125d5e..6109b95 100644 --- a/VcfRecordFactory.py +++ b/VcfRecordFactory.py @@ -92,7 +92,7 @@ def _get_identifier(self, bpm_record_group): if len(bpm_record_group) == 1: return bpm_record_group[0].name elif self._expand_identifiers: - return ",".join( + return ";".join( [bpm_record.name for bpm_record in bpm_record_group]) min_identifier_length = min( [len(bpm_record.name) for bpm_record in bpm_record_group]) From cad24b628b2cf560e9cac6c740d1a48c6908cc30 Mon Sep 17 00:00:00 2001 From: "Kelley, Ryan" Date: Wed, 28 Nov 2018 15:37:17 -0800 Subject: [PATCH 03/34] Update chromosome order to use reference Passing regression tests with Python 2 --- IlluminaBeadArrayFiles.py | 5 +- LocusEntryFactory.py | 6 +-- ReaderTemplateFactory.py | 7 +-- ReferenceGenome.py | 28 ++++++++++ gtc_to_vcf.py | 15 +----- tests/data/RegressionAux/output/output.vcf | 52 +++++++++---------- tests/data/RegressionBPM/output/output.vcf | 34 ++++++------ tests/data/RegressionCSV/output/output.vcf | 52 +++++++++---------- tests/data/RegressionGTC/output/output.vcf | 52 +++++++++---------- .../output/201142750001_R01C01.vcf | 52 +++++++++---------- .../output/201142750001_R01C02.vcf | 52 +++++++++---------- .../RegressionLociFilter/output/output.vcf | 52 +++++++++---------- 12 files changed, 213 insertions(+), 194 deletions(-) diff --git a/IlluminaBeadArrayFiles.py b/IlluminaBeadArrayFiles.py index 0e5af90..2736de3 100644 --- a/IlluminaBeadArrayFiles.py +++ b/IlluminaBeadArrayFiles.py @@ -597,13 +597,14 @@ def read_normalization_transform(handle): return NormalizationTransform(handle.read(52)) @staticmethod - def rect_to_polar(x,y): + def rect_to_polar(x_y): """Converts normalized x,y intensities to (pseudo) polar co-ordinates (R, theta) Args: - x,y (float, float): Normalized x,y intensities for probe + x_y (float, float): Normalized x,y intensities for probe Returns: (R,theta) polar values as tuple of floats """ + x,y = x_y if x == 0 and y == 0: return (nan, nan) return (x + y, arctan2(y,x) * 2.0 / pi) diff --git a/LocusEntryFactory.py b/LocusEntryFactory.py index 1e23f0e..9c03d0e 100644 --- a/LocusEntryFactory.py +++ b/LocusEntryFactory.py @@ -6,7 +6,7 @@ class LocusEntryFactory(object): Class to create locus entries from BPM records """ - def __init__(self, vcf_record_factory, chrom_sort_function, unsquash_duplicates, logger): + def __init__(self, vcf_record_factory, chrom_order, unsquash_duplicates, logger): """ Create new locus entry factory @@ -17,7 +17,7 @@ def __init__(self, vcf_record_factory, chrom_sort_function, unsquash_duplicates, logger (logging.Logger): Logger to report warnings/errors """ self._vcf_record_factory = vcf_record_factory - self._chrom_sort_function = chrom_sort_function + self._chrom_order = chrom_order self._unsquash_duplicates = unsquash_duplicates self._logger = logger @@ -36,7 +36,7 @@ def create_locus_entries(self, bpm_reader): result = [] for record_group in self._group_bpm_records(bpm_reader.get_bpm_records()): result.append(self._generate_locus_entry(record_group)) - return sorted(result, key=lambda entry: (self._chrom_sort_function(entry.vcf_record.CHROM), entry.vcf_record.POS, entry.vcf_record.REF)) + return sorted(result, key=lambda entry: (self._chrom_order[str(entry.vcf_record.CHROM)], entry.vcf_record.POS, entry.vcf_record.REF)) def _group_bpm_records(self, bpm_records): """ diff --git a/ReaderTemplateFactory.py b/ReaderTemplateFactory.py index d707b2f..97b8261 100644 --- a/ReaderTemplateFactory.py +++ b/ReaderTemplateFactory.py @@ -6,7 +6,7 @@ class ReaderTemplateFactory(object): """Class to create new reader templates""" - def __init__(self, genome_reader, format_factory, vcf_version, software_id, chrom_sort_function, logger): + def __init__(self, genome_reader, format_factory, vcf_version, software_id, chrom_order, logger): """Create new ReaderTemplateFactory Args @@ -14,6 +14,7 @@ def __init__(self, genome_reader, format_factory, vcf_version, software_id, chro format_factory (FormatFactory): FormatFactory to provide information about format_string vcf_version (string): version of VCF file software_id (string): identifier for software creating the VCF + chrom_order dict(string,int) : dictionary from contig to order chrom_sort_function(string): function definition used to sort chromosomes Returns ReaderTemplateFactory @@ -22,7 +23,7 @@ def __init__(self, genome_reader, format_factory, vcf_version, software_id, chro self._format_factory = format_factory self._vcf_version = vcf_version self._software_id = software_id - self._chrom_sort_function = chrom_sort_function + self._chrom_order = chrom_order self._contigs = {} self._logger = logger @@ -96,5 +97,5 @@ def create_header_contigs(self): else: contigs[contig_name] = _Contig(contig_name, length) contigs = OrderedDict( - sorted(contigs.items(), key=lambda x: self._chrom_sort_function(x[0]))) + sorted(contigs.items(), key=lambda x: self._chrom_order[str(x[0])])) return contigs diff --git a/ReferenceGenome.py b/ReferenceGenome.py index 72fbbed..7a4e7b3 100644 --- a/ReferenceGenome.py +++ b/ReferenceGenome.py @@ -58,6 +58,21 @@ def get_contig_lengths(self): """ return zip(self._fasta_file.references, self._fasta_file.lengths) + def get_contig_order(self): + """ + Get a dictionary with the ordering of the contigs + + Args: + None + + Returns: + dict(string,int): Return a dictionary mapping from contig name to order of that contig + """ + result = {} + for (idx, contig) in enumerate(self._fasta_file.references): + result[contig] = idx + return result + def get_reference_bases(self, chrom, start, end): """ Get the reference bases from start to end @@ -97,6 +112,7 @@ def __init__(self, reference_genome, logger): self._cache = CachedReferenceGenome.generate_genome_cache(reference_genome) self._logger.info("Finished caching reference data") self.genome_fasta_file = reference_genome.genome_fasta_file + self._contig_order = reference_genome.get_contig_order() @staticmethod def generate_genome_cache(reference_genome): @@ -114,6 +130,18 @@ def generate_genome_cache(reference_genome): result[contig] = reference_genome.get_reference_bases(contig, 0, contig_length) return result + def get_contig_order(self): + """ + Get a dictionary with the ordering of the contigs + + Args: + None + + Returns: + dict(string,int): Return a dictionary mapping from contig name to order of that contig + """ + return self._contig_order + def get_contig_lengths(self): """ Get the names and lengths of all contigs in a references diff --git a/gtc_to_vcf.py b/gtc_to_vcf.py index 14502b9..61a5b83 100755 --- a/gtc_to_vcf.py +++ b/gtc_to_vcf.py @@ -72,17 +72,6 @@ def verify_inputs(args): return errors - -CHROM_DICT = { - "X": 23, "Y": 24, "MT": 25 -} - -def chrom_sort(chrom_string): - """ Convert input chromosome string to appropriate type to ensure native - sort functions sorts chromosomes in order 1-22,X,Y,MT - """ - return int(chrom_string) if str(chrom_string).isdigit() else CHROM_DICT.get(chrom_string, 26) - def get_sample_name(gtc, gtc_file): sample_name = gtc.get_sample_name() if not sample_name: @@ -147,9 +136,9 @@ def read_auxiliary_records(auxiliary_loci): def driver(gtc_files, manifest_reader, genome_reader, output_vcf_files, expand_identifiers, unsquash_duplicates, auxiliary_records, logger): format_factory = FormatFactory(gtc_files[0] is None, logger) - reader_template_factory = ReaderTemplateFactory(genome_reader, format_factory, "4.1", "gtc_to_vcf " + VERSION, chrom_sort, logger) + reader_template_factory = ReaderTemplateFactory(genome_reader, format_factory, "4.1", "gtc_to_vcf " + VERSION, genome_reader.get_contig_order(), logger) vcf_record_factory = VcfRecordFactory(format_factory, genome_reader, expand_identifiers, auxiliary_records, logger) - locus_entries = LocusEntryFactory(vcf_record_factory, chrom_sort, unsquash_duplicates, logger).create_locus_entries(manifest_reader) + locus_entries = LocusEntryFactory(vcf_record_factory, genome_reader.get_contig_order(), unsquash_duplicates, logger).create_locus_entries(manifest_reader) for (gtc_file, output_vcf_file) in zip(gtc_files, output_vcf_files): if gtc_file: diff --git a/tests/data/RegressionAux/output/output.vcf b/tests/data/RegressionAux/output/output.vcf index 5cc31c4..c538096 100644 --- a/tests/data/RegressionAux/output/output.vcf +++ b/tests/data/RegressionAux/output/output.vcf @@ -1,6 +1,6 @@ ##fileformat=VCFv4.1 -##source=gtc_to_vcf 1.0.1 -##reference=file:///illumina/scratch/iGenomes/Homo_sapiens/NCBI/build37.2/Sequence/WholeGenomeFasta/genome.fa +##source=gtc_to_vcf 1.1.1 +##reference=file:///bioinfoSD/scratch/ryankelley/GTCtoVCF/tests/data/genome.fa ##contig= ##contig= ##contig= @@ -23,9 +23,9 @@ ##contig= ##contig= ##contig= -##contig= ##contig= ##contig= +##contig= #CHROM POS ID REF ALT QUAL FILTER INFO 1 1158675 1KG_1_1158675 C CCTT . PASS . 1 3542422 newrs148462952 GG TT . PASS . @@ -1955,29 +1955,6 @@ 22 43464415 newrs146662174 C T . PASS . 22 43926808 1KG_22_43926808 C CAGAGT . PASS . 22 45749876 1KG_22_45749876 G GC . PASS . -MT 125 200610-102 T C . PASS . -MT 212 200610-104 T C . PASS . -MT 236 200610-105 T C . PASS . -MT 482 200610-107 T C . PASS . -MT 3396 200610-111 T C . PASS . -MT 3644 200610-112 T C . PASS . -MT 3645 200610-113 T C . PASS . -MT 3826 200610-114 T C . PASS . -MT 5048 200610-119 T C . PASS . -MT 5108 200610-120 T C . PASS . -MT 6248 200610-121 T C . PASS . -MT 6392 200610-123 T C . PASS . -MT 7861 200610-127 T C . PASS . -MT 7870 200610-128 T C . PASS . -MT 7972 200610-13 A G . PASS . -MT 8502 200610-14 A G . PASS . -MT 10118 200610-133 T C . PASS . -MT 12121 200610-136 T C . PASS . -MT 12285 200610-137 T C . PASS . -MT 13215 200610-138 T C . PASS . -MT 15172 200610-100 G A . PASS . -MT 15514 200610-143 T C . PASS . -MT 16217 200610-146 T C . PASS . X 3241377 newrs150681202 C T . PASS . X 13734617 1KG_X_13734617 T TTTAG . PASS . X 21450738 1KG_X_21450738 C CT . PASS . @@ -2015,3 +1992,26 @@ X 152835147 newrs147874519 C T . PASS . X 153642450 newrs146934311 T C . PASS . X 153997508 newrs146700772 A C . PASS . X 154159071 newrs149853218 A C . PASS . +MT 125 200610-102 T C . PASS . +MT 212 200610-104 T C . PASS . +MT 236 200610-105 T C . PASS . +MT 482 200610-107 T C . PASS . +MT 3396 200610-111 T C . PASS . +MT 3644 200610-112 T C . PASS . +MT 3645 200610-113 T C . PASS . +MT 3826 200610-114 T C . PASS . +MT 5048 200610-119 T C . PASS . +MT 5108 200610-120 T C . PASS . +MT 6248 200610-121 T C . PASS . +MT 6392 200610-123 T C . PASS . +MT 7861 200610-127 T C . PASS . +MT 7870 200610-128 T C . PASS . +MT 7972 200610-13 A G . PASS . +MT 8502 200610-14 A G . PASS . +MT 10118 200610-133 T C . PASS . +MT 12121 200610-136 T C . PASS . +MT 12285 200610-137 T C . PASS . +MT 13215 200610-138 T C . PASS . +MT 15172 200610-100 G A . PASS . +MT 15514 200610-143 T C . PASS . +MT 16217 200610-146 T C . PASS . diff --git a/tests/data/RegressionBPM/output/output.vcf b/tests/data/RegressionBPM/output/output.vcf index 6fd7c2a..021376a 100644 --- a/tests/data/RegressionBPM/output/output.vcf +++ b/tests/data/RegressionBPM/output/output.vcf @@ -1,6 +1,6 @@ ##fileformat=VCFv4.1 -##source=gtc_to_vcf 1.0.1 -##reference=file:///illumina/scratch/iGenomes/Homo_sapiens/NCBI/build37.2/Sequence/WholeGenomeFasta/genome.fa +##source=gtc_to_vcf 1.1.1 +##reference=file:///bioinfoSD/scratch/ryankelley/GTCtoVCF/tests/data/genome.fa ##contig= ##contig= ##contig= @@ -23,9 +23,9 @@ ##contig= ##contig= ##contig= -##contig= ##contig= ##contig= +##contig= #CHROM POS ID REF ALT QUAL FILTER INFO 1 3542422 newrs148462952 G T . PASS . 1 3673329 newrs150537276 G T . PASS . @@ -994,6 +994,20 @@ 22 41605795 newrs146730690 G A . PASS . 22 41863452 newrs148099525 G A . PASS . 22 43464415 newrs146662174 C T . PASS . +X 3241377 newrs150681202 C T . PASS . +X 44950109 newrs148188315 A G . PASS . +X 62917005 newrs150129110 G A . PASS . +X 63445212 newrs148346736 G A . PASS . +X 73524476 newrs149628222 C A . PASS . +X 101091706 newrs146841797 C A . PASS . +X 106331799 newrs149164060 C T . PASS . +X 111698143 newrs148205998 C T . PASS . +X 134987551 newrs147659975 C T . PASS . +X 135095107 newrs149044510 C T . PASS . +X 152835147 newrs147874519 C T . PASS . +X 153642450 newrs146934311 T C . PASS . +X 153997508 newrs146700772 A C . PASS . +X 154159071 newrs149853218 A C . PASS . MT 125 200610-102 T C . PASS . MT 212 200610-104 T C . PASS . MT 236 200610-105 T C . PASS . @@ -1017,17 +1031,3 @@ MT 13215 200610-138 T C . PASS . MT 15172 200610-100 G A . PASS . MT 15514 200610-143 T C . PASS . MT 16217 200610-146 T C . PASS . -X 3241377 newrs150681202 C T . PASS . -X 44950109 newrs148188315 A G . PASS . -X 62917005 newrs150129110 G A . PASS . -X 63445212 newrs148346736 G A . PASS . -X 73524476 newrs149628222 C A . PASS . -X 101091706 newrs146841797 C A . PASS . -X 106331799 newrs149164060 C T . PASS . -X 111698143 newrs148205998 C T . PASS . -X 134987551 newrs147659975 C T . PASS . -X 135095107 newrs149044510 C T . PASS . -X 152835147 newrs147874519 C T . PASS . -X 153642450 newrs146934311 T C . PASS . -X 153997508 newrs146700772 A C . PASS . -X 154159071 newrs149853218 A C . PASS . diff --git a/tests/data/RegressionCSV/output/output.vcf b/tests/data/RegressionCSV/output/output.vcf index 1b0e35c..95b908e 100644 --- a/tests/data/RegressionCSV/output/output.vcf +++ b/tests/data/RegressionCSV/output/output.vcf @@ -1,6 +1,6 @@ ##fileformat=VCFv4.1 -##source=gtc_to_vcf 1.0.1 -##reference=file:///illumina/scratch/iGenomes/Homo_sapiens/NCBI/build37.2/Sequence/WholeGenomeFasta/genome.fa +##source=gtc_to_vcf 1.1.1 +##reference=file:///bioinfoSD/scratch/ryankelley/GTCtoVCF/tests/data/genome.fa ##contig= ##contig= ##contig= @@ -23,9 +23,9 @@ ##contig= ##contig= ##contig= -##contig= ##contig= ##contig= +##contig= #CHROM POS ID REF ALT QUAL FILTER INFO 1 1158675 1KG_1_1158675 C CCTT . PASS . 1 3542422 newrs148462952 G T . PASS . @@ -1955,29 +1955,6 @@ 22 43464415 newrs146662174 C T . PASS . 22 43926808 1KG_22_43926808 C CAGAGT . PASS . 22 45749876 1KG_22_45749876 G GC . PASS . -MT 125 200610-102 T C . PASS . -MT 212 200610-104 T C . PASS . -MT 236 200610-105 T C . PASS . -MT 482 200610-107 T C . PASS . -MT 3396 200610-111 T C . PASS . -MT 3644 200610-112 T C . PASS . -MT 3645 200610-113 T C . PASS . -MT 3826 200610-114 T C . PASS . -MT 5048 200610-119 T C . PASS . -MT 5108 200610-120 T C . PASS . -MT 6248 200610-121 T C . PASS . -MT 6392 200610-123 T C . PASS . -MT 7861 200610-127 T C . PASS . -MT 7870 200610-128 T C . PASS . -MT 7972 200610-13 A G . PASS . -MT 8502 200610-14 A G . PASS . -MT 10118 200610-133 T C . PASS . -MT 12121 200610-136 T C . PASS . -MT 12285 200610-137 T C . PASS . -MT 13215 200610-138 T C . PASS . -MT 15172 200610-100 G A . PASS . -MT 15514 200610-143 T C . PASS . -MT 16217 200610-146 T C . PASS . X 3241377 newrs150681202 C T . PASS . X 13734617 1KG_X_13734617 T TTTAG . PASS . X 21450738 1KG_X_21450738 C CT . PASS . @@ -2015,3 +1992,26 @@ X 152835147 newrs147874519 C T . PASS . X 153642450 newrs146934311 T C . PASS . X 153997508 newrs146700772 A C . PASS . X 154159071 newrs149853218 A C . PASS . +MT 125 200610-102 T C . PASS . +MT 212 200610-104 T C . PASS . +MT 236 200610-105 T C . PASS . +MT 482 200610-107 T C . PASS . +MT 3396 200610-111 T C . PASS . +MT 3644 200610-112 T C . PASS . +MT 3645 200610-113 T C . PASS . +MT 3826 200610-114 T C . PASS . +MT 5048 200610-119 T C . PASS . +MT 5108 200610-120 T C . PASS . +MT 6248 200610-121 T C . PASS . +MT 6392 200610-123 T C . PASS . +MT 7861 200610-127 T C . PASS . +MT 7870 200610-128 T C . PASS . +MT 7972 200610-13 A G . PASS . +MT 8502 200610-14 A G . PASS . +MT 10118 200610-133 T C . PASS . +MT 12121 200610-136 T C . PASS . +MT 12285 200610-137 T C . PASS . +MT 13215 200610-138 T C . PASS . +MT 15172 200610-100 G A . PASS . +MT 15514 200610-143 T C . PASS . +MT 16217 200610-146 T C . PASS . diff --git a/tests/data/RegressionGTC/output/output.vcf b/tests/data/RegressionGTC/output/output.vcf index 6e2fc30..b5d496e 100644 --- a/tests/data/RegressionGTC/output/output.vcf +++ b/tests/data/RegressionGTC/output/output.vcf @@ -1,6 +1,6 @@ ##fileformat=VCFv4.1 -##source=gtc_to_vcf 1.0.1 -##reference=file:///illumina/scratch/iGenomes/Homo_sapiens/NCBI/build37.2/Sequence/WholeGenomeFasta/genome.fa +##source=gtc_to_vcf 1.1.1 +##reference=file:///bioinfoSD/scratch/ryankelley/GTCtoVCF/tests/data/genome.fa ##FORMAT= ##FORMAT= ##contig= @@ -25,9 +25,9 @@ ##contig= ##contig= ##contig= -##contig= ##contig= ##contig= +##contig= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12753 1 1158675 1KG_1_1158675 C CCTT . PASS . GT:GQ 0/0:0.437028 1 3542422 newrs148462952 G T . PASS . GT:GQ 0/0:0.470694 @@ -1957,29 +1957,6 @@ 22 43464415 newrs146662174 C T . PASS . GT:GQ 0/0:0.500205 22 43926808 1KG_22_43926808 C CAGAGT . PASS . GT:GQ 0/0:0.516234 22 45749876 1KG_22_45749876 G GC . PASS . GT:GQ 0/0:0.473406 -MT 125 200610-102 T C . PASS . GT:GQ 0:0.446263 -MT 212 200610-104 T C . PASS . GT:GQ 0:0.398159 -MT 236 200610-105 T C . PASS . GT:GQ 0:0.648628 -MT 482 200610-107 T C . PASS . GT:GQ 0:0.812968 -MT 3396 200610-111 T C . PASS . GT:GQ 0:0.666947 -MT 3644 200610-112 T C . PASS . GT:GQ 0:0.361595 -MT 3645 200610-113 T C . PASS . GT:GQ 0:0.374745 -MT 3826 200610-114 T C . PASS . GT:GQ 0:0.374745 -MT 5048 200610-119 T C . PASS . GT:GQ 0:0.35256 -MT 5108 200610-120 T C . PASS . GT:GQ 0:0.310474 -MT 6248 200610-121 T C . PASS . GT:GQ 0:0.361595 -MT 6392 200610-123 T C . PASS . GT:GQ 0:0.480041 -MT 7861 200610-127 T C . PASS . GT:GQ 0:0.242924 -MT 7870 200610-128 T C . PASS . GT:GQ 0:0.312218 -MT 7972 200610-13 A G . PASS . GT:GQ 0:0.335269 -MT 8502 200610-14 A G . PASS . GT:GQ 0:0.500205 -MT 10118 200610-133 T C . PASS . GT:GQ 0:0.376958 -MT 12121 200610-136 T C . PASS . GT:GQ 0:0.376958 -MT 12285 200610-137 T C . PASS . GT:GQ 0:0.440272 -MT 13215 200610-138 T C . PASS . GT:GQ 0:0.384898 -MT 15172 200610-100 G A . PASS . GT:GQ 0:0.219084 -MT 15514 200610-143 T C . PASS . GT:GQ 0:0.648628 -MT 16217 200610-146 T C . PASS . GT:GQ 0:0.436944 X 3241377 newrs150681202 C T . PASS . GT:GQ 0:0.401561 X 13734617 1KG_X_13734617 T TTTAG . PASS . GT:GQ 0:0.392839 X 21450738 1KG_X_21450738 C CT . PASS . GT:GQ 0:0.497315 @@ -2017,3 +1994,26 @@ X 152835147 newrs147874519 C T . PASS . GT:GQ 0:0.386838 X 153642450 newrs146934311 T C . PASS . GT:GQ 0:0.632201 X 153997508 newrs146700772 A C . PASS . GT:GQ 0:0.446295 X 154159071 newrs149853218 A C . PASS . GT:GQ 0:0.831019 +MT 125 200610-102 T C . PASS . GT:GQ 0:0.446263 +MT 212 200610-104 T C . PASS . GT:GQ 0:0.398159 +MT 236 200610-105 T C . PASS . GT:GQ 0:0.648628 +MT 482 200610-107 T C . PASS . GT:GQ 0:0.812968 +MT 3396 200610-111 T C . PASS . GT:GQ 0:0.666947 +MT 3644 200610-112 T C . PASS . GT:GQ 0:0.361595 +MT 3645 200610-113 T C . PASS . GT:GQ 0:0.374745 +MT 3826 200610-114 T C . PASS . GT:GQ 0:0.374745 +MT 5048 200610-119 T C . PASS . GT:GQ 0:0.35256 +MT 5108 200610-120 T C . PASS . GT:GQ 0:0.310474 +MT 6248 200610-121 T C . PASS . GT:GQ 0:0.361595 +MT 6392 200610-123 T C . PASS . GT:GQ 0:0.480041 +MT 7861 200610-127 T C . PASS . GT:GQ 0:0.242924 +MT 7870 200610-128 T C . PASS . GT:GQ 0:0.312218 +MT 7972 200610-13 A G . PASS . GT:GQ 0:0.335269 +MT 8502 200610-14 A G . PASS . GT:GQ 0:0.500205 +MT 10118 200610-133 T C . PASS . GT:GQ 0:0.376958 +MT 12121 200610-136 T C . PASS . GT:GQ 0:0.376958 +MT 12285 200610-137 T C . PASS . GT:GQ 0:0.440272 +MT 13215 200610-138 T C . PASS . GT:GQ 0:0.384898 +MT 15172 200610-100 G A . PASS . GT:GQ 0:0.219084 +MT 15514 200610-143 T C . PASS . GT:GQ 0:0.648628 +MT 16217 200610-146 T C . PASS . GT:GQ 0:0.436944 diff --git a/tests/data/RegressionGTCDirectory/output/201142750001_R01C01.vcf b/tests/data/RegressionGTCDirectory/output/201142750001_R01C01.vcf index 6e2fc30..b5d496e 100644 --- a/tests/data/RegressionGTCDirectory/output/201142750001_R01C01.vcf +++ b/tests/data/RegressionGTCDirectory/output/201142750001_R01C01.vcf @@ -1,6 +1,6 @@ ##fileformat=VCFv4.1 -##source=gtc_to_vcf 1.0.1 -##reference=file:///illumina/scratch/iGenomes/Homo_sapiens/NCBI/build37.2/Sequence/WholeGenomeFasta/genome.fa +##source=gtc_to_vcf 1.1.1 +##reference=file:///bioinfoSD/scratch/ryankelley/GTCtoVCF/tests/data/genome.fa ##FORMAT= ##FORMAT= ##contig= @@ -25,9 +25,9 @@ ##contig= ##contig= ##contig= -##contig= ##contig= ##contig= +##contig= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12753 1 1158675 1KG_1_1158675 C CCTT . PASS . GT:GQ 0/0:0.437028 1 3542422 newrs148462952 G T . PASS . GT:GQ 0/0:0.470694 @@ -1957,29 +1957,6 @@ 22 43464415 newrs146662174 C T . PASS . GT:GQ 0/0:0.500205 22 43926808 1KG_22_43926808 C CAGAGT . PASS . GT:GQ 0/0:0.516234 22 45749876 1KG_22_45749876 G GC . PASS . GT:GQ 0/0:0.473406 -MT 125 200610-102 T C . PASS . GT:GQ 0:0.446263 -MT 212 200610-104 T C . PASS . GT:GQ 0:0.398159 -MT 236 200610-105 T C . PASS . GT:GQ 0:0.648628 -MT 482 200610-107 T C . PASS . GT:GQ 0:0.812968 -MT 3396 200610-111 T C . PASS . GT:GQ 0:0.666947 -MT 3644 200610-112 T C . PASS . GT:GQ 0:0.361595 -MT 3645 200610-113 T C . PASS . GT:GQ 0:0.374745 -MT 3826 200610-114 T C . PASS . GT:GQ 0:0.374745 -MT 5048 200610-119 T C . PASS . GT:GQ 0:0.35256 -MT 5108 200610-120 T C . PASS . GT:GQ 0:0.310474 -MT 6248 200610-121 T C . PASS . GT:GQ 0:0.361595 -MT 6392 200610-123 T C . PASS . GT:GQ 0:0.480041 -MT 7861 200610-127 T C . PASS . GT:GQ 0:0.242924 -MT 7870 200610-128 T C . PASS . GT:GQ 0:0.312218 -MT 7972 200610-13 A G . PASS . GT:GQ 0:0.335269 -MT 8502 200610-14 A G . PASS . GT:GQ 0:0.500205 -MT 10118 200610-133 T C . PASS . GT:GQ 0:0.376958 -MT 12121 200610-136 T C . PASS . GT:GQ 0:0.376958 -MT 12285 200610-137 T C . PASS . GT:GQ 0:0.440272 -MT 13215 200610-138 T C . PASS . GT:GQ 0:0.384898 -MT 15172 200610-100 G A . PASS . GT:GQ 0:0.219084 -MT 15514 200610-143 T C . PASS . GT:GQ 0:0.648628 -MT 16217 200610-146 T C . PASS . GT:GQ 0:0.436944 X 3241377 newrs150681202 C T . PASS . GT:GQ 0:0.401561 X 13734617 1KG_X_13734617 T TTTAG . PASS . GT:GQ 0:0.392839 X 21450738 1KG_X_21450738 C CT . PASS . GT:GQ 0:0.497315 @@ -2017,3 +1994,26 @@ X 152835147 newrs147874519 C T . PASS . GT:GQ 0:0.386838 X 153642450 newrs146934311 T C . PASS . GT:GQ 0:0.632201 X 153997508 newrs146700772 A C . PASS . GT:GQ 0:0.446295 X 154159071 newrs149853218 A C . PASS . GT:GQ 0:0.831019 +MT 125 200610-102 T C . PASS . GT:GQ 0:0.446263 +MT 212 200610-104 T C . PASS . GT:GQ 0:0.398159 +MT 236 200610-105 T C . PASS . GT:GQ 0:0.648628 +MT 482 200610-107 T C . PASS . GT:GQ 0:0.812968 +MT 3396 200610-111 T C . PASS . GT:GQ 0:0.666947 +MT 3644 200610-112 T C . PASS . GT:GQ 0:0.361595 +MT 3645 200610-113 T C . PASS . GT:GQ 0:0.374745 +MT 3826 200610-114 T C . PASS . GT:GQ 0:0.374745 +MT 5048 200610-119 T C . PASS . GT:GQ 0:0.35256 +MT 5108 200610-120 T C . PASS . GT:GQ 0:0.310474 +MT 6248 200610-121 T C . PASS . GT:GQ 0:0.361595 +MT 6392 200610-123 T C . PASS . GT:GQ 0:0.480041 +MT 7861 200610-127 T C . PASS . GT:GQ 0:0.242924 +MT 7870 200610-128 T C . PASS . GT:GQ 0:0.312218 +MT 7972 200610-13 A G . PASS . GT:GQ 0:0.335269 +MT 8502 200610-14 A G . PASS . GT:GQ 0:0.500205 +MT 10118 200610-133 T C . PASS . GT:GQ 0:0.376958 +MT 12121 200610-136 T C . PASS . GT:GQ 0:0.376958 +MT 12285 200610-137 T C . PASS . GT:GQ 0:0.440272 +MT 13215 200610-138 T C . PASS . GT:GQ 0:0.384898 +MT 15172 200610-100 G A . PASS . GT:GQ 0:0.219084 +MT 15514 200610-143 T C . PASS . GT:GQ 0:0.648628 +MT 16217 200610-146 T C . PASS . GT:GQ 0:0.436944 diff --git a/tests/data/RegressionGTCDirectory/output/201142750001_R01C02.vcf b/tests/data/RegressionGTCDirectory/output/201142750001_R01C02.vcf index 6e2fc30..b5d496e 100644 --- a/tests/data/RegressionGTCDirectory/output/201142750001_R01C02.vcf +++ b/tests/data/RegressionGTCDirectory/output/201142750001_R01C02.vcf @@ -1,6 +1,6 @@ ##fileformat=VCFv4.1 -##source=gtc_to_vcf 1.0.1 -##reference=file:///illumina/scratch/iGenomes/Homo_sapiens/NCBI/build37.2/Sequence/WholeGenomeFasta/genome.fa +##source=gtc_to_vcf 1.1.1 +##reference=file:///bioinfoSD/scratch/ryankelley/GTCtoVCF/tests/data/genome.fa ##FORMAT= ##FORMAT= ##contig= @@ -25,9 +25,9 @@ ##contig= ##contig= ##contig= -##contig= ##contig= ##contig= +##contig= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12753 1 1158675 1KG_1_1158675 C CCTT . PASS . GT:GQ 0/0:0.437028 1 3542422 newrs148462952 G T . PASS . GT:GQ 0/0:0.470694 @@ -1957,29 +1957,6 @@ 22 43464415 newrs146662174 C T . PASS . GT:GQ 0/0:0.500205 22 43926808 1KG_22_43926808 C CAGAGT . PASS . GT:GQ 0/0:0.516234 22 45749876 1KG_22_45749876 G GC . PASS . GT:GQ 0/0:0.473406 -MT 125 200610-102 T C . PASS . GT:GQ 0:0.446263 -MT 212 200610-104 T C . PASS . GT:GQ 0:0.398159 -MT 236 200610-105 T C . PASS . GT:GQ 0:0.648628 -MT 482 200610-107 T C . PASS . GT:GQ 0:0.812968 -MT 3396 200610-111 T C . PASS . GT:GQ 0:0.666947 -MT 3644 200610-112 T C . PASS . GT:GQ 0:0.361595 -MT 3645 200610-113 T C . PASS . GT:GQ 0:0.374745 -MT 3826 200610-114 T C . PASS . GT:GQ 0:0.374745 -MT 5048 200610-119 T C . PASS . GT:GQ 0:0.35256 -MT 5108 200610-120 T C . PASS . GT:GQ 0:0.310474 -MT 6248 200610-121 T C . PASS . GT:GQ 0:0.361595 -MT 6392 200610-123 T C . PASS . GT:GQ 0:0.480041 -MT 7861 200610-127 T C . PASS . GT:GQ 0:0.242924 -MT 7870 200610-128 T C . PASS . GT:GQ 0:0.312218 -MT 7972 200610-13 A G . PASS . GT:GQ 0:0.335269 -MT 8502 200610-14 A G . PASS . GT:GQ 0:0.500205 -MT 10118 200610-133 T C . PASS . GT:GQ 0:0.376958 -MT 12121 200610-136 T C . PASS . GT:GQ 0:0.376958 -MT 12285 200610-137 T C . PASS . GT:GQ 0:0.440272 -MT 13215 200610-138 T C . PASS . GT:GQ 0:0.384898 -MT 15172 200610-100 G A . PASS . GT:GQ 0:0.219084 -MT 15514 200610-143 T C . PASS . GT:GQ 0:0.648628 -MT 16217 200610-146 T C . PASS . GT:GQ 0:0.436944 X 3241377 newrs150681202 C T . PASS . GT:GQ 0:0.401561 X 13734617 1KG_X_13734617 T TTTAG . PASS . GT:GQ 0:0.392839 X 21450738 1KG_X_21450738 C CT . PASS . GT:GQ 0:0.497315 @@ -2017,3 +1994,26 @@ X 152835147 newrs147874519 C T . PASS . GT:GQ 0:0.386838 X 153642450 newrs146934311 T C . PASS . GT:GQ 0:0.632201 X 153997508 newrs146700772 A C . PASS . GT:GQ 0:0.446295 X 154159071 newrs149853218 A C . PASS . GT:GQ 0:0.831019 +MT 125 200610-102 T C . PASS . GT:GQ 0:0.446263 +MT 212 200610-104 T C . PASS . GT:GQ 0:0.398159 +MT 236 200610-105 T C . PASS . GT:GQ 0:0.648628 +MT 482 200610-107 T C . PASS . GT:GQ 0:0.812968 +MT 3396 200610-111 T C . PASS . GT:GQ 0:0.666947 +MT 3644 200610-112 T C . PASS . GT:GQ 0:0.361595 +MT 3645 200610-113 T C . PASS . GT:GQ 0:0.374745 +MT 3826 200610-114 T C . PASS . GT:GQ 0:0.374745 +MT 5048 200610-119 T C . PASS . GT:GQ 0:0.35256 +MT 5108 200610-120 T C . PASS . GT:GQ 0:0.310474 +MT 6248 200610-121 T C . PASS . GT:GQ 0:0.361595 +MT 6392 200610-123 T C . PASS . GT:GQ 0:0.480041 +MT 7861 200610-127 T C . PASS . GT:GQ 0:0.242924 +MT 7870 200610-128 T C . PASS . GT:GQ 0:0.312218 +MT 7972 200610-13 A G . PASS . GT:GQ 0:0.335269 +MT 8502 200610-14 A G . PASS . GT:GQ 0:0.500205 +MT 10118 200610-133 T C . PASS . GT:GQ 0:0.376958 +MT 12121 200610-136 T C . PASS . GT:GQ 0:0.376958 +MT 12285 200610-137 T C . PASS . GT:GQ 0:0.440272 +MT 13215 200610-138 T C . PASS . GT:GQ 0:0.384898 +MT 15172 200610-100 G A . PASS . GT:GQ 0:0.219084 +MT 15514 200610-143 T C . PASS . GT:GQ 0:0.648628 +MT 16217 200610-146 T C . PASS . GT:GQ 0:0.436944 diff --git a/tests/data/RegressionLociFilter/output/output.vcf b/tests/data/RegressionLociFilter/output/output.vcf index 1c1f9e0..3ae9a57 100644 --- a/tests/data/RegressionLociFilter/output/output.vcf +++ b/tests/data/RegressionLociFilter/output/output.vcf @@ -1,6 +1,6 @@ ##fileformat=VCFv4.1 -##source=gtc_to_vcf 1.0.1+dev3 -##reference=file:///illumina/scratch/iGenomes/Homo_sapiens/NCBI/build37.2/Sequence/WholeGenomeFasta/genome.fa +##source=gtc_to_vcf 1.1.1 +##reference=file:///bioinfoSD/scratch/ryankelley/GTCtoVCF/tests/data/genome.fa ##contig= ##contig= ##contig= @@ -23,9 +23,9 @@ ##contig= ##contig= ##contig= -##contig= ##contig= ##contig= +##contig= #CHROM POS ID REF ALT QUAL FILTER INFO 1 1158675 1KG_1_1158675 C CCTT . PASS . 1 3542422 newrs148462952 G T . PASS . @@ -1953,29 +1953,6 @@ 22 43464415 newrs146662174 C T . PASS . 22 43926808 1KG_22_43926808 C CAGAGT . PASS . 22 45749876 1KG_22_45749876 G GC . PASS . -MT 125 200610-102 T C . PASS . -MT 212 200610-104 T C . PASS . -MT 236 200610-105 T C . PASS . -MT 482 200610-107 T C . PASS . -MT 3396 200610-111 T C . PASS . -MT 3644 200610-112 T C . PASS . -MT 3645 200610-113 T C . PASS . -MT 3826 200610-114 T C . PASS . -MT 5048 200610-119 T C . PASS . -MT 5108 200610-120 T C . PASS . -MT 6248 200610-121 T C . PASS . -MT 6392 200610-123 T C . PASS . -MT 7861 200610-127 T C . PASS . -MT 7870 200610-128 T C . PASS . -MT 7972 200610-13 A G . PASS . -MT 8502 200610-14 A G . PASS . -MT 10118 200610-133 T C . PASS . -MT 12121 200610-136 T C . PASS . -MT 12285 200610-137 T C . PASS . -MT 13215 200610-138 T C . PASS . -MT 15172 200610-100 G A . PASS . -MT 15514 200610-143 T C . PASS . -MT 16217 200610-146 T C . PASS . X 3241377 newrs150681202 C T . PASS . X 13734617 1KG_X_13734617 T TTTAG . PASS . X 21450738 1KG_X_21450738 C CT . PASS . @@ -2013,3 +1990,26 @@ X 152835147 newrs147874519 C T . PASS . X 153642450 newrs146934311 T C . PASS . X 153997508 newrs146700772 A C . PASS . X 154159071 newrs149853218 A C . PASS . +MT 125 200610-102 T C . PASS . +MT 212 200610-104 T C . PASS . +MT 236 200610-105 T C . PASS . +MT 482 200610-107 T C . PASS . +MT 3396 200610-111 T C . PASS . +MT 3644 200610-112 T C . PASS . +MT 3645 200610-113 T C . PASS . +MT 3826 200610-114 T C . PASS . +MT 5048 200610-119 T C . PASS . +MT 5108 200610-120 T C . PASS . +MT 6248 200610-121 T C . PASS . +MT 6392 200610-123 T C . PASS . +MT 7861 200610-127 T C . PASS . +MT 7870 200610-128 T C . PASS . +MT 7972 200610-13 A G . PASS . +MT 8502 200610-14 A G . PASS . +MT 10118 200610-133 T C . PASS . +MT 12121 200610-136 T C . PASS . +MT 12285 200610-137 T C . PASS . +MT 13215 200610-138 T C . PASS . +MT 15172 200610-100 G A . PASS . +MT 15514 200610-143 T C . PASS . +MT 16217 200610-146 T C . PASS . From 667cd14e7c8a319e7bb184d465826268fe3d14fa Mon Sep 17 00:00:00 2001 From: "Kelley, Ryan" Date: Wed, 28 Nov 2018 19:56:28 -0800 Subject: [PATCH 04/34] string vs byte issues --- GenotypeFormat.py | 3 +-- IlluminaBeadArrayFiles.py | 2 +- gtc_to_vcf.py | 2 +- tests/test_class.py | 2 +- 4 files changed, 4 insertions(+), 5 deletions(-) diff --git a/GenotypeFormat.py b/GenotypeFormat.py index 6e45b77..a67063a 100644 --- a/GenotypeFormat.py +++ b/GenotypeFormat.py @@ -13,9 +13,8 @@ def get_expected_ploidy(gender, chrom): Returns int: value of expected ploidy, currently set at 1 or 2 """ - if (gender == "M" and chrom == "X") or chrom == "Y" or chrom == "MT": + if (gender == b"M" and chrom == "X") or chrom == "Y" or chrom == "MT": return 1 - return 2 diff --git a/IlluminaBeadArrayFiles.py b/IlluminaBeadArrayFiles.py index 2736de3..5bf2115 100644 --- a/IlluminaBeadArrayFiles.py +++ b/IlluminaBeadArrayFiles.py @@ -705,7 +705,7 @@ def __parse_file(self, manifest_file): """ with open(manifest_file, "rb") as manifest_handle: header = manifest_handle.read(3) - if len(header) != 3 or header != "BPM": + if len(header) != 3 or header != b"BPM": raise Exception("Invalid BPM format") version = read_byte(manifest_handle) if version != 1: diff --git a/gtc_to_vcf.py b/gtc_to_vcf.py index 61a5b83..588f691 100755 --- a/gtc_to_vcf.py +++ b/gtc_to_vcf.py @@ -128,7 +128,7 @@ def read_auxiliary_records(auxiliary_loci): """ if auxiliary_loci is not None: auxiliary_records = {} - with open(auxiliary_loci, "rb") as auxiliary_handle: + with open(auxiliary_loci, "rt") as auxiliary_handle: for record in Reader(auxiliary_handle): auxiliary_records[record.ID] = record return auxiliary_records diff --git a/tests/test_class.py b/tests/test_class.py index fe5c323..787a33b 100644 --- a/tests/test_class.py +++ b/tests/test_class.py @@ -101,7 +101,7 @@ def check_genotype(self, data, expected_genotype): records[idx].index_num = idx genotypes = [datum[1] for datum in data] combiner = RecordCombiner(records, genotypes, "") - self.assertEqual(combiner.combine_genotypes(), expected_genotype) + self.assertEqual(sorted(combiner.combine_genotypes()), sorted(expected_genotype)) def test_genotype_combination(self): logger = Logger("test_genotype_combinations") From 64488bfc57d7e3d18981dd9ea97c8ec79e4bc565 Mon Sep 17 00:00:00 2001 From: ryankelley Date: Mon, 10 Dec 2018 07:21:36 -0800 Subject: [PATCH 05/34] Address review comments update changelog change delimiter modify shebang line --- VcfRecordFactory.py | 2 +- changelog.md | 5 +++++ gtc_to_vcf.py | 2 +- 3 files changed, 7 insertions(+), 2 deletions(-) diff --git a/VcfRecordFactory.py b/VcfRecordFactory.py index 3125d5e..6109b95 100644 --- a/VcfRecordFactory.py +++ b/VcfRecordFactory.py @@ -92,7 +92,7 @@ def _get_identifier(self, bpm_record_group): if len(bpm_record_group) == 1: return bpm_record_group[0].name elif self._expand_identifiers: - return ",".join( + return ";".join( [bpm_record.name for bpm_record in bpm_record_group]) min_identifier_length = min( [len(bpm_record.name) for bpm_record in bpm_record_group]) diff --git a/changelog.md b/changelog.md index 3614b38..0cee326 100644 --- a/changelog.md +++ b/changelog.md @@ -1,3 +1,8 @@ +# Development +* Python3 compatibility fixes +* Use chromosome ordering from reference +* Use semi-colon as delimiter within identifier field + # 1.1.1 (2018/03/27) * Output warning if any mismatch to reference genome in indel source sequence * Count length of indel when scoring deletion reference allele diff --git a/gtc_to_vcf.py b/gtc_to_vcf.py index 588f691..733cc5c 100755 --- a/gtc_to_vcf.py +++ b/gtc_to_vcf.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python2 +#!/usr/bin/env python import os import sys From d4e2942a2b9b441374e8d1727e6e22b5aa98536a Mon Sep 17 00:00:00 2001 From: eyherabh Date: Thu, 13 Dec 2018 08:34:06 +0200 Subject: [PATCH 06/34] Few typos and missing punctuation. --- README.md | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 6e32e9b..7e3414d 100644 --- a/README.md +++ b/README.md @@ -58,17 +58,17 @@ The --output-vcf-path option may either be a file or directory. If the argument ### Manifests The supplied manifest file may either be in CSV or BPM format; however, a CSV format manifest is required to generate indel records in the output VCF. When running the converter with a BPM manifest, indel processing must be explicitly disabled with the "--skip-indels" option. In either case, the manifest must provide RefStrand annotations. The GTC to VCF converter depends on the presence of accurate mapping information within the manifest, and may produce inaccurate results if the mapping information is incorrect. Mapping information should follow the implicit dbSNP standard, where -* Positions are reported with 1-based indexing -* Positions in the PAR are reported with mapping position to the X chromosome -* For an insertion relative to the reference, the position of the base immediately 5' to the insertion (on the plus strand) is given -* For a deletion relative to the reference, the position of most 5' deleted based (on the plus strand) is given +* Positions are reported with 1-based indexing. +* Positions in the PAR are reported with mapping position to the X chromosome. +* For an insertion relative to the reference, the position of the base immediately 5' to the insertion (on the plus strand) is given. +* For a deletion relative to the reference, the position of the most 5' deleted based (on the plus strand) is given. Any standard product manifest provided by Illumina will already follow these conventions. ### Reference genome The contig identifiers in the provided genome FASTA file must match exactly the chromosome identifiers specified in the provided manifest. For a standard human product manifest, this means that the contig headers should read ">1" rather than ">chr1". For compatibility with BaseSpace Variant Interpreter (https://www.illumina.com/informatics/research/biological-data-interpretation/variant-interpreter.html), the specified path of the reference must contain either contain the string GrCh37 or GrCh38, for build 37 and 38, respectively. Suitable whole genome FASTA files can be built with the download_reference.sh script located within the scripts directory. ### Squashing duplicates -In the manifest, there can be cases where the same variant is probed by multiple different assays. These assays may be the same design or alternate designs for the same locus. In the default mode of operation, these duplicates will be "squashed" into a single record in the VCF. The method used to incorporate information across multiple assays is under the latter "Output description" heading. When the "--unsquash-duplicates" option is provided, this "squashing" behavior is disabled, and each duplicate assay will be reported in a separate entry in the VCF file. This option is helpful when you are interested in investigating or validating the performance of individual assays, rather than trying to generate genotypes for specific variants. Note that if an locus has more than two alleles and is also queried with duplicated designs, the duplicates will not be unsquashed. +In the manifest, there can be cases where the same variant is probed by multiple different assays. These assays may be the same design or alternate designs for the same locus. In the default mode of operation, these duplicates will be "squashed" into a single record in the VCF. The method used to incorporate information across multiple assays is under the latter "Output description" heading. When the "--unsquash-duplicates" option is provided, this "squashing" behavior is disabled, and each duplicate assay will be reported in a separate entry in the VCF file. This option is helpful when you are interested in investigating or validating the performance of individual assays, rather than trying to generate genotypes for specific variants. Note that if a locus has more than two alleles and is also queried with duplicated designs, the duplicates will not be unsquashed. ### Genome cache By default, the entire reference genome will be read into memory. Generally, this will be more efficient than reading data from the indexed reference on disk at the expense of greater memory utilization. For situations in which the genome caching is not desirable (low memory availability or a small input manifest), it is possible to disable this default behavior with the "--disable-genome-cache" option. @@ -83,9 +83,9 @@ This assay could be designed as a SNP assay with the following source sequence ATGC[A/C]NNNN The GTC converter tool provides an option to supply a list of auxiliary records (in VCF format) to restore the true alleles for these cases in the output VCF. There are several restrictions around this function -* The auxiliary definition must be bi-allelic -* The auxiliary definition must be a multi-nucleotide variant -* There must not be multiple array assays (e.g., duplicates) for the locus +* The auxiliary definition must be bi-allelic. +* The auxiliary definition must be a multi-nucleotide variant. +* There must not be multiple array assays (e.g., duplicates) for the locus. ## Output description The VCF file output follows VCF4.1 format (https://samtools.github.io/hts-specs/VCFv4.1.pdf). Some additional details on output formatting: From dc68b1f9c6a7ec833a05966eb211071f2c765437 Mon Sep 17 00:00:00 2001 From: eyherabh Date: Mon, 17 Dec 2018 08:10:13 +0200 Subject: [PATCH 07/34] Possible error in comment on last test The comment on the last test did not seem to coincide with what was being actually tested, and looked more like a copy of the comment on the previous test. I corrected it taking as an example the fourth to last test. --- tests/test_class.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/test_class.py b/tests/test_class.py index 787a33b..8a9f290 100644 --- a/tests/test_class.py +++ b/tests/test_class.py @@ -205,9 +205,9 @@ def test_genotype_combination(self): data.append((BPMRecord("", None, None, "", 0, "[T/G]", RefStrand.Plus, 1, None, None, None, None, 1, logger), 2)) self.check_genotype(data, ('T', 'G')) - # Inf II [A/G] -> AG - # Inf I [T/G] -> TG - # TG + # Inf II [A/G] -> AA + # Inf I [T/G] -> TT + # -- data = [] data.append((BPMRecord("", None, None, "", 0, "[A/G]", RefStrand.Plus, 0, None, None, None, None, 1, logger), 1)) data.append((BPMRecord("", None, None, "", 0, "[T/G]", RefStrand.Plus, 1, None, None, None, None, 1, logger), 1)) From ac25b9743ec7840caa3626497096558ad22f0e5c Mon Sep 17 00:00:00 2001 From: eyherabh Date: Mon, 17 Dec 2018 09:21:59 +0200 Subject: [PATCH 08/34] Typo in comment on BPMRecord name was repeated twice, but I believe the second time should have been address_a instead. --- BPMRecord.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/BPMRecord.py b/BPMRecord.py index ddbb846..d0e181d 100644 --- a/BPMRecord.py +++ b/BPMRecord.py @@ -87,7 +87,7 @@ def __init__(self, name, address_a, probe_a, chromosome, pos, snp, ref_strand, a Args: name (string) : Name field from manifest - name (string) : AddressA_ID field from manifest + address_a (string) : AddressA_ID field from manifest probe_a (string) : AlleleA_ProbeSeq field from manifest chromosome (string) : Chr field from manifest pos (string, int) : MapInfo field from manifest From 0e1b598fd6c1b56a274914a03a4ac5064341eb4a Mon Sep 17 00:00:00 2001 From: Guus van de Steeg <45566691+GvandeSteeg@users.noreply.github.com> Date: Mon, 14 Jan 2019 13:23:37 +0000 Subject: [PATCH 09/34] Update download_reference.sh Convert `realpath` to `readlink -f`, which might be more generally supported on UNIX --- scripts/download_reference.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/scripts/download_reference.sh b/scripts/download_reference.sh index 14b5542..8f267c3 100644 --- a/scripts/download_reference.sh +++ b/scripts/download_reference.sh @@ -6,7 +6,7 @@ then exit 1 fi -output_file=`realpath ${1}` +output_file=`readlink -f ${1}` output_dir=`dirname ${output_file}` genome_build=${2:-"37"} @@ -40,4 +40,4 @@ else fi popd -rm -r ${temp_dir} \ No newline at end of file +rm -r ${temp_dir} From cf1dc48d4cb60f212dc018f4646dfb33aa59e747 Mon Sep 17 00:00:00 2001 From: Brian Hill Date: Fri, 20 Jul 2018 14:28:49 -0700 Subject: [PATCH 10/34] Initial code for creating FORMAT fields for additional fields --- BAlleleFreqFormat.py | 36 ++++++++++++++++++++++++++++++++++++ FormatFactory.py | 9 +++++++++ ThetaFormat.py | 34 ++++++++++++++++++++++++++++++++++ 3 files changed, 79 insertions(+) create mode 100644 BAlleleFreqFormat.py create mode 100644 ThetaFormat.py diff --git a/BAlleleFreqFormat.py b/BAlleleFreqFormat.py new file mode 100644 index 0000000..8eda75e --- /dev/null +++ b/BAlleleFreqFormat.py @@ -0,0 +1,36 @@ +from vcf.parser import _Format + + +class BAlleleFreqFormat(object): + """ + Generate b allele frequency format information for VCF + """ + def __init__(self, logger, b_allele_freq): + self._b_allele_freq = b_allele_freq + self._logger = logger + + @staticmethod + def get_id(): + return "BAF" + + @staticmethod + def get_description(): + return "B Allele Frequency" + + @staticmethod + def get_format_obj(): + # arguments should be: ['id', 'num', 'type', 'desc'] + return _Format(BAlleleFreqFormat.get_id(), 1, "Float", BAlleleFreqFormat.get_description()) + + def generate_sample_format_info(self, bpm_records, vcf_record, sample_name): + """ + Get the sample b allele frequency + + Args: + + Returns: + float: B allele frequency + """ + # TODO: we need to handle the case where there are multiple BPMs + idx = bpm_records[0].index_num + return self._b_allele_freq[idx] diff --git a/FormatFactory.py b/FormatFactory.py index 427cb12..8ac650e 100644 --- a/FormatFactory.py +++ b/FormatFactory.py @@ -1,5 +1,7 @@ from GenotypeFormat import GenotypeFormat from GencallFormat import GencallFormat +from ThetaFormat import ThetaFormat +from BAlleleFreqFormat import BAlleleFreqFormat class FormatFactory(object): """FormatFactory is responsible for determining the fields @@ -22,6 +24,8 @@ def __init__(self, no_samples, logger): if not no_samples: self._format_classes.append(GenotypeFormat) self._format_classes.append(GencallFormat) + self._format_classes.append(ThetaFormat) + self._format_classes.append(BAlleleFreqFormat) def get_format_id_string(self): """ @@ -74,4 +78,9 @@ def create_formats(self, gtc): self._logger, gtc.get_gender(), gtc.get_genotypes())) result.append(GencallFormat( self._logger, gtc.get_genotype_scores())) + # TODO: figure out how to get Theta value (.get_call_rate is just placeholder) + result.append(ThetaFormat( + self._logger, gtc.get_call_rate())) + result.append(BAlleleFreqFormat( + self._logger, gtc.get_ballele_freqs())) return result diff --git a/ThetaFormat.py b/ThetaFormat.py new file mode 100644 index 0000000..02d0548 --- /dev/null +++ b/ThetaFormat.py @@ -0,0 +1,34 @@ +from vcf.parser import _Format + + +class ThetaFormat(object): + """ + Generate Theta format information for VCF + """ + def __init__(self, logger, theta): + self._theta = theta + self._logger = logger + + @staticmethod + def get_id(): + return "TH" + + @staticmethod + def get_description(): + return "Normalized Theta-value for the sample" + + @staticmethod + def get_format_obj(): + # arguments should be: ['id', 'num', 'type', 'desc'] + return _Format(ThetaFormat.get_id(), 1, "Float", ThetaFormat.get_description()) + + def generate_sample_format_info(self, bpm_records, vcf_record, sample_name): + """ + Get the sample genotype + + Args: + + Returns: + float: Theta value + """ + return self._theta From 16989225ceee69e491add985f944861ed54d7b3a Mon Sep 17 00:00:00 2001 From: Brian Hill Date: Mon, 23 Jul 2018 13:41:28 -0700 Subject: [PATCH 11/34] Added code for extracting Log R ratio --- LogRRatioFormat.py | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 LogRRatioFormat.py diff --git a/LogRRatioFormat.py b/LogRRatioFormat.py new file mode 100644 index 0000000..7b247c7 --- /dev/null +++ b/LogRRatioFormat.py @@ -0,0 +1,36 @@ +from vcf.parser import _Format + + +class LogRRatioFormat(object): + """ + Generate log R ratio format information for VCF + """ + def __init__(self, logger, log_r_ratio): + self._log_r_ratio = log_r_ratio + self._logger = logger + + @staticmethod + def get_id(): + return "LRR" + + @staticmethod + def get_description(): + return "Log R Ratio" + + @staticmethod + def get_format_obj(): + # arguments should be: ['id', 'num', 'type', 'desc'] + return _Format(LogRRatioFormat.get_id(), 1, "Float", LogRRatioFormat.get_description()) + + def generate_sample_format_info(self, bpm_records, vcf_record, sample_name): + """ + Get the sample log R ratio + + Args: + + Returns: + float: log R ratio + """ + # TODO: we need to handle the case where there are multiple BPMs + idx = bpm_records[0].index_num + return self._log_r_ratio[idx] From 51695daba339ea8ebbf4ae32913fadc4390f3cc5 Mon Sep 17 00:00:00 2001 From: Brian Hill Date: Mon, 23 Jul 2018 14:47:06 -0700 Subject: [PATCH 12/34] Added additional command line argument --include-attributes for specifying additional FORMAT attribute fields to include in the VCF file --- FormatFactory.py | 46 ++++++++++++++++++++++++++++++++-------------- gtc_to_vcf.py | 16 ++++++++++++---- 2 files changed, 44 insertions(+), 18 deletions(-) diff --git a/FormatFactory.py b/FormatFactory.py index 8ac650e..bf6d27b 100644 --- a/FormatFactory.py +++ b/FormatFactory.py @@ -2,6 +2,8 @@ from GencallFormat import GencallFormat from ThetaFormat import ThetaFormat from BAlleleFreqFormat import BAlleleFreqFormat +from LogRRatioFormat import LogRRatioFormat + class FormatFactory(object): """FormatFactory is responsible for determining the fields @@ -9,23 +11,31 @@ class FormatFactory(object): the appropriate corresponding format objects """ - def __init__(self, no_samples, logger): + def __init__(self, no_samples, formats_to_include, logger): """ Create a new FormatFactory Args: no_samples (bool): True iff no sample data is present (format string should be empty) + formats_to_include list(String): list of FORMAT IDs to include (default: GT,GC) Returns: FormatFactory """ self._logger = logger self._format_classes = [] + self._formats_to_include = formats_to_include if not no_samples: - self._format_classes.append(GenotypeFormat) - self._format_classes.append(GencallFormat) - self._format_classes.append(ThetaFormat) - self._format_classes.append(BAlleleFreqFormat) + if GenotypeFormat.get_id() in formats_to_include: + self._format_classes.append(GenotypeFormat) + if GencallFormat.get_id() in formats_to_include: + self._format_classes.append(GencallFormat) + if ThetaFormat.get_id() in formats_to_include: + self._format_classes.append(ThetaFormat) + if BAlleleFreqFormat.get_id() in formats_to_include: + self._format_classes.append(BAlleleFreqFormat) + if LogRRatioFormat.get_id() in formats_to_include: + self._format_classes.append(LogRRatioFormat) def get_format_id_string(self): """ @@ -74,13 +84,21 @@ def create_formats(self, gtc): None """ result = [] - result.append(GenotypeFormat( - self._logger, gtc.get_gender(), gtc.get_genotypes())) - result.append(GencallFormat( - self._logger, gtc.get_genotype_scores())) - # TODO: figure out how to get Theta value (.get_call_rate is just placeholder) - result.append(ThetaFormat( - self._logger, gtc.get_call_rate())) - result.append(BAlleleFreqFormat( - self._logger, gtc.get_ballele_freqs())) + # only append if ID is in command line args + if GenotypeFormat.get_id() in self._formats_to_include: + result.append(GenotypeFormat( + self._logger, gtc.get_gender(), gtc.get_genotypes())) + if GencallFormat.get_id() in self._formats_to_include: + result.append(GencallFormat( + self._logger, gtc.get_genotype_scores())) + if ThetaFormat.get_id() in self._formats_to_include: + result.append(ThetaFormat( + self._logger, gtc)) + if BAlleleFreqFormat.get_id() in self._formats_to_include: + result.append(BAlleleFreqFormat( + self._logger, gtc.get_ballele_freqs())) + if LogRRatioFormat.get_id() in self._formats_to_include: + result.append(LogRRatioFormat( + self._logger, gtc.get_logr_ratios())) + return result diff --git a/gtc_to_vcf.py b/gtc_to_vcf.py index 733cc5c..be12d82 100755 --- a/gtc_to_vcf.py +++ b/gtc_to_vcf.py @@ -134,9 +134,9 @@ def read_auxiliary_records(auxiliary_loci): return auxiliary_records return None -def driver(gtc_files, manifest_reader, genome_reader, output_vcf_files, expand_identifiers, unsquash_duplicates, auxiliary_records, logger): - format_factory = FormatFactory(gtc_files[0] is None, logger) - reader_template_factory = ReaderTemplateFactory(genome_reader, format_factory, "4.1", "gtc_to_vcf " + VERSION, genome_reader.get_contig_order(), logger) +def driver(gtc_files, manifest_reader, genome_reader, output_vcf_files, expand_identifiers, unsquash_duplicates, auxiliary_records, attrs_to_include, logger): + format_factory = FormatFactory(gtc_files[0] is None, attrs_to_include, logger) + reader_template_factory = ReaderTemplateFactory(genome_reader, format_factory, "4.1", "gtc_to_vcf " + VERSION, chrom_sort, logger) vcf_record_factory = VcfRecordFactory(format_factory, genome_reader, expand_identifiers, auxiliary_records, logger) locus_entries = LocusEntryFactory(vcf_record_factory, genome_reader.get_contig_order(), unsquash_duplicates, logger).create_locus_entries(manifest_reader) @@ -280,6 +280,7 @@ def main(): parser.add_argument("--auxiliary-loci", dest="auxiliary_loci", default=None, required=False, help="VCF file with auxiliary definitions of loci (optional)") parser.add_argument("--filter-loci", dest="filter_loci", default=None, required=False, help="File containing list of loci names to filter from input manifest (optional)") parser.add_argument("--disable-genome-cache", dest="disable_genome_cache", default=False, action="store_true", help="Disable caching of genome reference data") + parser.add_argument("--include-attributes", dest="include_attributes", default=[], choices=["TH","BAF","LRR"], nargs="*", help="Attributes to include in VCF FORMAT output (default: ['GT', 'GQ']") parser.add_argument("--version", action="version", version='%(prog)s ' + VERSION) args = parser.parse_args() @@ -287,6 +288,13 @@ def main(): args.manifest_file = os.path.abspath(args.manifest_file) args.genome_fasta_file = os.path.abspath(args.genome_fasta_file) + if args.include_attributes is None: + args.include_attributes = ["GT", "GQ"] + else: + args.include_attributes.append("GT") + args.include_attributes.append("GQ") + print "Attrs:", args.include_attributes + logger = get_logger() add_file_logger(logger, args.log_file) errors = verify_inputs(args) @@ -305,7 +313,7 @@ def main(): manifest_reader = get_manifest_reader(args.manifest_file, genome_reader, loci_to_filter, args.skip_indels, logger) auxiliary_records = read_auxiliary_records(args.auxiliary_loci) - driver(gtc_paths, manifest_reader, genome_reader, output_vcf_files, args.expand_identifiers, args.unsquash_duplicates, auxiliary_records, logger) + driver(gtc_paths, manifest_reader, genome_reader, output_vcf_files, args.expand_identifiers, args.unsquash_duplicates, auxiliary_records, args.include_attributes, logger) except Exception as exception: logger.error(str(exception)) logger.debug(traceback.format_exc(exception)) From 2b71c25e179d02807253c8d375fc6b3e22823167 Mon Sep 17 00:00:00 2001 From: Brian Hill Date: Mon, 23 Jul 2018 14:51:42 -0700 Subject: [PATCH 13/34] Added command line flag to README.md --- README.md | 4 ++++ gtc_to_vcf.py | 2 +- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 7e3414d..dceeb84 100644 --- a/README.md +++ b/README.md @@ -9,6 +9,7 @@ usage: gtc_to_vcf.py [-h] [--gtc-paths GTC_PATHS [GTC_PATHS ...]] [--expand-identifiers] [--unsquash-duplicates] [--auxiliary-loci AUXILIARY_LOCI] [--filter-loci FILTER_LOCI] [--disable-genome-cache] + [--include-attributes [{TH,BAF,LRR} [{TH,BAF,LRR} ...]]] [--version] Convert GTC file to VCF format @@ -37,6 +38,9 @@ optional arguments: input manifest (optional) --disable-genome-cache Disable caching of genome reference data + --include-attributes [{TH,BAF,LRR} [{TH,BAF,LRR} ...]] + Additional attributes to include in VCF FORMAT output + (optional) --version show program's version number and exit diff --git a/gtc_to_vcf.py b/gtc_to_vcf.py index be12d82..456fef0 100755 --- a/gtc_to_vcf.py +++ b/gtc_to_vcf.py @@ -280,7 +280,7 @@ def main(): parser.add_argument("--auxiliary-loci", dest="auxiliary_loci", default=None, required=False, help="VCF file with auxiliary definitions of loci (optional)") parser.add_argument("--filter-loci", dest="filter_loci", default=None, required=False, help="File containing list of loci names to filter from input manifest (optional)") parser.add_argument("--disable-genome-cache", dest="disable_genome_cache", default=False, action="store_true", help="Disable caching of genome reference data") - parser.add_argument("--include-attributes", dest="include_attributes", default=[], choices=["TH","BAF","LRR"], nargs="*", help="Attributes to include in VCF FORMAT output (default: ['GT', 'GQ']") + parser.add_argument("--include-attributes", dest="include_attributes", default=[], choices=["TH","BAF","LRR"], nargs="*", help="Additional attributes to include in VCF FORMAT output (optional)") parser.add_argument("--version", action="version", version='%(prog)s ' + VERSION) args = parser.parse_args() From 97285de82655cec384563c4871ee092a785b0ce3 Mon Sep 17 00:00:00 2001 From: Brian Hill Date: Wed, 25 Jul 2018 17:19:54 -0700 Subject: [PATCH 14/34] Removed ThetaFormat.py --- ThetaFormat.py | 34 ---------------------------------- 1 file changed, 34 deletions(-) delete mode 100644 ThetaFormat.py diff --git a/ThetaFormat.py b/ThetaFormat.py deleted file mode 100644 index 02d0548..0000000 --- a/ThetaFormat.py +++ /dev/null @@ -1,34 +0,0 @@ -from vcf.parser import _Format - - -class ThetaFormat(object): - """ - Generate Theta format information for VCF - """ - def __init__(self, logger, theta): - self._theta = theta - self._logger = logger - - @staticmethod - def get_id(): - return "TH" - - @staticmethod - def get_description(): - return "Normalized Theta-value for the sample" - - @staticmethod - def get_format_obj(): - # arguments should be: ['id', 'num', 'type', 'desc'] - return _Format(ThetaFormat.get_id(), 1, "Float", ThetaFormat.get_description()) - - def generate_sample_format_info(self, bpm_records, vcf_record, sample_name): - """ - Get the sample genotype - - Args: - - Returns: - float: Theta value - """ - return self._theta From 73c24ee4e5ae2ca7793194c1bd50aad2f18e4d0c Mon Sep 17 00:00:00 2001 From: Brian Hill Date: Wed, 25 Jul 2018 17:22:37 -0700 Subject: [PATCH 15/34] Removed references to Theta --- README.md | 2 +- gtc_to_vcf.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index dceeb84..6dde6c4 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ usage: gtc_to_vcf.py [-h] [--gtc-paths GTC_PATHS [GTC_PATHS ...]] [--expand-identifiers] [--unsquash-duplicates] [--auxiliary-loci AUXILIARY_LOCI] [--filter-loci FILTER_LOCI] [--disable-genome-cache] - [--include-attributes [{TH,BAF,LRR} [{TH,BAF,LRR} ...]]] + [--include-attributes [{BAF,LRR} [{BAF,LRR} ...]]] [--version] Convert GTC file to VCF format diff --git a/gtc_to_vcf.py b/gtc_to_vcf.py index 456fef0..2d4a183 100755 --- a/gtc_to_vcf.py +++ b/gtc_to_vcf.py @@ -280,7 +280,7 @@ def main(): parser.add_argument("--auxiliary-loci", dest="auxiliary_loci", default=None, required=False, help="VCF file with auxiliary definitions of loci (optional)") parser.add_argument("--filter-loci", dest="filter_loci", default=None, required=False, help="File containing list of loci names to filter from input manifest (optional)") parser.add_argument("--disable-genome-cache", dest="disable_genome_cache", default=False, action="store_true", help="Disable caching of genome reference data") - parser.add_argument("--include-attributes", dest="include_attributes", default=[], choices=["TH","BAF","LRR"], nargs="*", help="Additional attributes to include in VCF FORMAT output (optional)") + parser.add_argument("--include-attributes", dest="include_attributes", default=[], choices=["BAF","LRR"], nargs="*", help="Additional attributes to include in VCF FORMAT output (optional)") parser.add_argument("--version", action="version", version='%(prog)s ' + VERSION) args = parser.parse_args() From 8a3fb91caac7367b23f42da948390c3c01b57785 Mon Sep 17 00:00:00 2001 From: Brian Hill Date: Fri, 10 Aug 2018 17:56:01 -0700 Subject: [PATCH 16/34] First set of changes for merging B allele frequency from multiple BPMRecords --- BAlleleFreqFormat.py | 89 ++++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 85 insertions(+), 4 deletions(-) diff --git a/BAlleleFreqFormat.py b/BAlleleFreqFormat.py index 8eda75e..6d78680 100644 --- a/BAlleleFreqFormat.py +++ b/BAlleleFreqFormat.py @@ -1,4 +1,40 @@ from vcf.parser import _Format +import numpy as np + +REVERSE_COMPLIMENT = {"A": "T", "T": "A", "G": "C", "C": "G"} + + +def extract_alleles_from_snp_string(snp_string): + """ + Splits SNP string into tuple of individual alleles + + Args: snp_string (string): allele string of the format + [T/C] or [G/C] + + Returns: + allele1 (string), allele2 (string) + """ + (allele1, allele2) = snp_string[1:4].split("/") + assert allele1 in "ATGC" + assert allele2 in "ATGC" + return allele1, allele2 + + +def normalize_alleles_by_strand(snp_string): + """ + Splits SNP string into tuple of individual alleles and + gets takes the reverse compliment to match strand 1 + + Args: snp_string (string): allele string of the format + [T/C] or [G/C] + + Returns: + allele1 (string), allele2 (string) + """ + # get alleles as tuple + allele1, allele2 = extract_alleles_from_snp_string(snp_string) + # get reverse compliment of bases and return + return REVERSE_COMPLIMENT[allele1], REVERSE_COMPLIMENT[allele2] class BAlleleFreqFormat(object): @@ -24,13 +60,58 @@ def get_format_obj(): def generate_sample_format_info(self, bpm_records, vcf_record, sample_name): """ - Get the sample b allele frequency + Get the sample B allele frequency Args: Returns: float: B allele frequency """ - # TODO: we need to handle the case where there are multiple BPMs - idx = bpm_records[0].index_num - return self._b_allele_freq[idx] + # if we have more than 1 BPMRecord, need to merge + b_allele_freq_list = [] + if len(bpm_records) > 1: + # if we have more than 1 alt allele, return missing + if len(vcf_record.ALT) > 1: + return "." + for i in range(len(bpm_records)): + snp = bpm_records[i].snp + strand = bpm_records[i].ref_strand + + idx = bpm_records[i].index_num + b_allele_freq = self._b_allele_freq[idx] + # if second strand, normalize strand + if strand == 1: + allele1, allele2 = extract_alleles_from_snp_string(snp) + else: + allele1, allele2 = normalize_alleles_by_strand(snp) + + # normalize to reference allele + ref_allele = vcf_record.REF + # if allele1 is reference, then B allele is correct + if allele1 == ref_allele: + b_allele_freq_list.append(b_allele_freq) + # if allele2 is reference, then we need to do 1-freq + elif allele2 == ref_allele: + b_allele_freq_list.append(1. - b_allele_freq) + + #chrom = bpm_records[i].chromosome + #start_pos = bpm_records[i].pos + #alt_allele = vcf_record.ALT + #print("chr: {} pos: {} ref: {} alt: {} snp: {} strand: {} BAF: {}".format(chrom, start_pos, ref_allele, alt_allele, snp, strand, b_allele_freq)) + + #print(b_allele_freq_list) + + # otherwise single BPMRecord + else: + # if we have a multi-allelic site, return missing + if len(vcf_record.ALT) > 1: + return "." + idx = bpm_records[0].index_num + b_allele_freq_list.append(self._b_allele_freq[idx]) + + # nanmedian ignores NaN values + final_b_allele_freq = np.nanmedian(b_allele_freq_list) + if np.isnan(final_b_allele_freq): + return "." + else: + return final_b_allele_freq From 03d29f66ddd8012e498cc4583d752fac703d3b65 Mon Sep 17 00:00:00 2001 From: Brian Hill Date: Tue, 14 Aug 2018 12:20:31 -0700 Subject: [PATCH 17/34] Added code for merging Log R Ratio values from multiple BPMRecords --- LogRRatioFormat.py | 38 +++++++++++++++++++++++++++++++++++--- 1 file changed, 35 insertions(+), 3 deletions(-) diff --git a/LogRRatioFormat.py b/LogRRatioFormat.py index 7b247c7..27d3839 100644 --- a/LogRRatioFormat.py +++ b/LogRRatioFormat.py @@ -1,4 +1,5 @@ from vcf.parser import _Format +import numpy as np class LogRRatioFormat(object): @@ -31,6 +32,37 @@ def generate_sample_format_info(self, bpm_records, vcf_record, sample_name): Returns: float: log R ratio """ - # TODO: we need to handle the case where there are multiple BPMs - idx = bpm_records[0].index_num - return self._log_r_ratio[idx] + # if we have more than 1 BPMRecord, need to merge + log_r_ratio_list = [] + if len(bpm_records) > 1: + # if we have more than 1 alt allele, return missing + if len(vcf_record.ALT) > 1: + return "." + for i in range(len(bpm_records)): + idx = bpm_records[i].index_num + log_r_ratio = self._log_r_ratio[idx] + log_r_ratio_list.append(log_r_ratio) + + # snp = bpm_records[i].snp + # strand = bpm_records[i].ref_strand + # ref_allele = vcf_record.REF + + # chrom = bpm_records[i].chromosome + # start_pos = bpm_records[i].pos + # alt_allele = vcf_record.ALT + # print("chr: {} pos: {} ref: {} alt: {} snp: {} strand: {} LRR: {}".format(chrom, start_pos, ref_allele, alt_allele, snp, strand, log_r_ratio)) + + # otherwise single BPMRecord + else: + # if we have a multi-allelic site, return missing + if len(vcf_record.ALT) > 1: + return "." + idx = bpm_records[0].index_num + log_r_ratio_list.append(self._log_r_ratio[idx]) + + # nanmedian ignores NaN values + final_log_r_ratio = np.nanmedian(log_r_ratio_list) + if np.isnan(final_log_r_ratio): + return "." + else: + return final_log_r_ratio From c2d569da466d13be6db69a58f6837d3176f2a44d Mon Sep 17 00:00:00 2001 From: Brian Hill Date: Tue, 14 Aug 2018 12:22:05 -0700 Subject: [PATCH 18/34] Removed reference to ThetaFormat --- FormatFactory.py | 1 - 1 file changed, 1 deletion(-) diff --git a/FormatFactory.py b/FormatFactory.py index bf6d27b..8b45304 100644 --- a/FormatFactory.py +++ b/FormatFactory.py @@ -1,6 +1,5 @@ from GenotypeFormat import GenotypeFormat from GencallFormat import GencallFormat -from ThetaFormat import ThetaFormat from BAlleleFreqFormat import BAlleleFreqFormat from LogRRatioFormat import LogRRatioFormat From 98ceded8402a2f314dc98f53a90bf96fa39b82b1 Mon Sep 17 00:00:00 2001 From: Brian Hill Date: Tue, 14 Aug 2018 12:23:14 -0700 Subject: [PATCH 19/34] Removed reference to Theta (TH) --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 6dde6c4..2b569d5 100644 --- a/README.md +++ b/README.md @@ -38,7 +38,7 @@ optional arguments: input manifest (optional) --disable-genome-cache Disable caching of genome reference data - --include-attributes [{TH,BAF,LRR} [{TH,BAF,LRR} ...]] + --include-attributes [{BAF,LRR} [{BAF,LRR} ...]] Additional attributes to include in VCF FORMAT output (optional) --version show program's version number and exit From 5c1bd090a1592cd82c9f4a9c3db76f7ba6980f22 Mon Sep 17 00:00:00 2001 From: Brian Hill Date: Tue, 14 Aug 2018 12:30:58 -0700 Subject: [PATCH 20/34] Found and removed one more mention of ThetaFactory --- FormatFactory.py | 5 ----- 1 file changed, 5 deletions(-) diff --git a/FormatFactory.py b/FormatFactory.py index 8b45304..36976dc 100644 --- a/FormatFactory.py +++ b/FormatFactory.py @@ -29,8 +29,6 @@ def __init__(self, no_samples, formats_to_include, logger): self._format_classes.append(GenotypeFormat) if GencallFormat.get_id() in formats_to_include: self._format_classes.append(GencallFormat) - if ThetaFormat.get_id() in formats_to_include: - self._format_classes.append(ThetaFormat) if BAlleleFreqFormat.get_id() in formats_to_include: self._format_classes.append(BAlleleFreqFormat) if LogRRatioFormat.get_id() in formats_to_include: @@ -90,9 +88,6 @@ def create_formats(self, gtc): if GencallFormat.get_id() in self._formats_to_include: result.append(GencallFormat( self._logger, gtc.get_genotype_scores())) - if ThetaFormat.get_id() in self._formats_to_include: - result.append(ThetaFormat( - self._logger, gtc)) if BAlleleFreqFormat.get_id() in self._formats_to_include: result.append(BAlleleFreqFormat( self._logger, gtc.get_ballele_freqs())) From 1d6606cf3c99cf0fda0dbca0fd874162a2e57b5d Mon Sep 17 00:00:00 2001 From: Brian Hill Date: Mon, 20 Aug 2018 12:42:38 -0700 Subject: [PATCH 21/34] Changed attribute options to static list in the FormatFactory, and default list is now GT,GQ --- FormatFactory.py | 10 ++++++++++ README.md | 4 ++-- gtc_to_vcf.py | 9 +-------- 3 files changed, 13 insertions(+), 10 deletions(-) diff --git a/FormatFactory.py b/FormatFactory.py index 36976dc..c302924 100644 --- a/FormatFactory.py +++ b/FormatFactory.py @@ -23,6 +23,8 @@ def __init__(self, no_samples, formats_to_include, logger): """ self._logger = logger self._format_classes = [] + for fmt in formats_to_include: + assert fmt in FormatFactory.get_possible_formats(), "%r is not a valid FORMAT" % fmt self._formats_to_include = formats_to_include if not no_samples: if GenotypeFormat.get_id() in formats_to_include: @@ -34,6 +36,14 @@ def __init__(self, no_samples, formats_to_include, logger): if LogRRatioFormat.get_id() in formats_to_include: self._format_classes.append(LogRRatioFormat) + @staticmethod + def get_possible_formats(): + valid_classes = [GenotypeFormat.get_id(), + GencallFormat.get_id(), + BAlleleFreqFormat.get_id(), + LogRRatioFormat.get_id()] + return valid_classes + def get_format_id_string(self): """ Get the concatenated string of all format IDs diff --git a/README.md b/README.md index 2b569d5..4e98ca5 100644 --- a/README.md +++ b/README.md @@ -38,9 +38,9 @@ optional arguments: input manifest (optional) --disable-genome-cache Disable caching of genome reference data - --include-attributes [{BAF,LRR} [{BAF,LRR} ...]] + --include-attributes [{GT,GQ,BAF,LRR} [{GT,GQ,BAF,LRR} ...]] Additional attributes to include in VCF FORMAT output - (optional) + (optional) (default is GT GQ) --version show program's version number and exit diff --git a/gtc_to_vcf.py b/gtc_to_vcf.py index 2d4a183..46bc796 100755 --- a/gtc_to_vcf.py +++ b/gtc_to_vcf.py @@ -280,7 +280,7 @@ def main(): parser.add_argument("--auxiliary-loci", dest="auxiliary_loci", default=None, required=False, help="VCF file with auxiliary definitions of loci (optional)") parser.add_argument("--filter-loci", dest="filter_loci", default=None, required=False, help="File containing list of loci names to filter from input manifest (optional)") parser.add_argument("--disable-genome-cache", dest="disable_genome_cache", default=False, action="store_true", help="Disable caching of genome reference data") - parser.add_argument("--include-attributes", dest="include_attributes", default=[], choices=["BAF","LRR"], nargs="*", help="Additional attributes to include in VCF FORMAT output (optional)") + parser.add_argument("--include-attributes", dest="include_attributes", default=["GT", "GQ"], choices=FormatFactory.get_possible_formats(), nargs="*", help="Additional attributes to include in VCF FORMAT output (optional)") parser.add_argument("--version", action="version", version='%(prog)s ' + VERSION) args = parser.parse_args() @@ -288,13 +288,6 @@ def main(): args.manifest_file = os.path.abspath(args.manifest_file) args.genome_fasta_file = os.path.abspath(args.genome_fasta_file) - if args.include_attributes is None: - args.include_attributes = ["GT", "GQ"] - else: - args.include_attributes.append("GT") - args.include_attributes.append("GQ") - print "Attrs:", args.include_attributes - logger = get_logger() add_file_logger(logger, args.log_file) errors = verify_inputs(args) From 4db37702cb2e56bee57b55f4ba5b5c30eed7f845 Mon Sep 17 00:00:00 2001 From: Brian Hill Date: Fri, 5 Oct 2018 13:40:28 -0700 Subject: [PATCH 22/34] Refactored code to not use separate cases for single record and multiple records --- BAlleleFreqFormat.py | 70 ++++++++++++++++++-------------------------- LogRRatioFormat.py | 32 +++++--------------- README.md | 2 +- 3 files changed, 37 insertions(+), 67 deletions(-) diff --git a/BAlleleFreqFormat.py b/BAlleleFreqFormat.py index 6d78680..09b6ef6 100644 --- a/BAlleleFreqFormat.py +++ b/BAlleleFreqFormat.py @@ -1,4 +1,5 @@ from vcf.parser import _Format +from IlluminaBeadArrayFiles import RefStrand import numpy as np REVERSE_COMPLIMENT = {"A": "T", "T": "A", "G": "C", "C": "G"} @@ -15,8 +16,8 @@ def extract_alleles_from_snp_string(snp_string): allele1 (string), allele2 (string) """ (allele1, allele2) = snp_string[1:4].split("/") - assert allele1 in "ATGC" - assert allele2 in "ATGC" + # assert allele1 in "ATGC", "allele %r is invalid (expected A,T,G,C)" % allele1 + # assert allele2 in "ATGC", "allele %r is invalid (expected A,T,G,C)" % allele2 return allele1, allele2 @@ -69,45 +70,32 @@ def generate_sample_format_info(self, bpm_records, vcf_record, sample_name): """ # if we have more than 1 BPMRecord, need to merge b_allele_freq_list = [] - if len(bpm_records) > 1: - # if we have more than 1 alt allele, return missing - if len(vcf_record.ALT) > 1: - return "." - for i in range(len(bpm_records)): - snp = bpm_records[i].snp - strand = bpm_records[i].ref_strand - - idx = bpm_records[i].index_num - b_allele_freq = self._b_allele_freq[idx] - # if second strand, normalize strand - if strand == 1: - allele1, allele2 = extract_alleles_from_snp_string(snp) - else: - allele1, allele2 = normalize_alleles_by_strand(snp) - - # normalize to reference allele - ref_allele = vcf_record.REF - # if allele1 is reference, then B allele is correct - if allele1 == ref_allele: - b_allele_freq_list.append(b_allele_freq) - # if allele2 is reference, then we need to do 1-freq - elif allele2 == ref_allele: - b_allele_freq_list.append(1. - b_allele_freq) - - #chrom = bpm_records[i].chromosome - #start_pos = bpm_records[i].pos - #alt_allele = vcf_record.ALT - #print("chr: {} pos: {} ref: {} alt: {} snp: {} strand: {} BAF: {}".format(chrom, start_pos, ref_allele, alt_allele, snp, strand, b_allele_freq)) - - #print(b_allele_freq_list) - - # otherwise single BPMRecord - else: - # if we have a multi-allelic site, return missing - if len(vcf_record.ALT) > 1: - return "." - idx = bpm_records[0].index_num - b_allele_freq_list.append(self._b_allele_freq[idx]) + # if we have more than 1 alt allele, return missing + if len(vcf_record.ALT) > 1: + return "." + for i in range(len(bpm_records)): + snp = bpm_records[i].snp + print(snp) + strand = bpm_records[i].ref_strand + + idx = bpm_records[i].index_num + b_allele_freq = self._b_allele_freq[idx] + # if second (minus) strand, normalize strand + if strand == RefStrand.Minus: + allele1, allele2 = normalize_alleles_by_strand(snp) + else: + allele1, allele2 = extract_alleles_from_snp_string(snp) + + # normalize to reference allele + ref_allele = vcf_record.REF + # if allele1 is reference, then B allele is correct + if allele1 == ref_allele: + b_allele_freq_list.append(b_allele_freq) + # if allele2 is reference, then we need to do 1-freq + elif allele2 == ref_allele: + b_allele_freq_list.append(1. - b_allele_freq) + else: + print("ref allele: {} allele1: {} allele2: {}".format(ref_allele, allele1, allele2)) # nanmedian ignores NaN values final_b_allele_freq = np.nanmedian(b_allele_freq_list) diff --git a/LogRRatioFormat.py b/LogRRatioFormat.py index 27d3839..a51f5c8 100644 --- a/LogRRatioFormat.py +++ b/LogRRatioFormat.py @@ -34,31 +34,13 @@ def generate_sample_format_info(self, bpm_records, vcf_record, sample_name): """ # if we have more than 1 BPMRecord, need to merge log_r_ratio_list = [] - if len(bpm_records) > 1: - # if we have more than 1 alt allele, return missing - if len(vcf_record.ALT) > 1: - return "." - for i in range(len(bpm_records)): - idx = bpm_records[i].index_num - log_r_ratio = self._log_r_ratio[idx] - log_r_ratio_list.append(log_r_ratio) - - # snp = bpm_records[i].snp - # strand = bpm_records[i].ref_strand - # ref_allele = vcf_record.REF - - # chrom = bpm_records[i].chromosome - # start_pos = bpm_records[i].pos - # alt_allele = vcf_record.ALT - # print("chr: {} pos: {} ref: {} alt: {} snp: {} strand: {} LRR: {}".format(chrom, start_pos, ref_allele, alt_allele, snp, strand, log_r_ratio)) - - # otherwise single BPMRecord - else: - # if we have a multi-allelic site, return missing - if len(vcf_record.ALT) > 1: - return "." - idx = bpm_records[0].index_num - log_r_ratio_list.append(self._log_r_ratio[idx]) + # if we have more than 1 alt allele, return missing + if len(vcf_record.ALT) > 1: + return "." + for i in range(len(bpm_records)): + idx = bpm_records[i].index_num + log_r_ratio = self._log_r_ratio[idx] + log_r_ratio_list.append(log_r_ratio) # nanmedian ignores NaN values final_log_r_ratio = np.nanmedian(log_r_ratio_list) diff --git a/README.md b/README.md index 4e98ca5..53bcd97 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ usage: gtc_to_vcf.py [-h] [--gtc-paths GTC_PATHS [GTC_PATHS ...]] [--expand-identifiers] [--unsquash-duplicates] [--auxiliary-loci AUXILIARY_LOCI] [--filter-loci FILTER_LOCI] [--disable-genome-cache] - [--include-attributes [{BAF,LRR} [{BAF,LRR} ...]]] + [--include-attributes [{GT,GQ,BAF,LRR} [{GT,GQ,BAF,LRR} ...]]] [--version] Convert GTC file to VCF format From e8692486d2245e7f7da08ca64194f886148bedd7 Mon Sep 17 00:00:00 2001 From: Jake Zieve Date: Thu, 9 May 2019 15:44:15 -0700 Subject: [PATCH 23/34] Removes print statement, add assertion --- BAlleleFreqFormat.py | 6 ++---- gtc_to_vcf.py | 8 +++++++- 2 files changed, 9 insertions(+), 5 deletions(-) diff --git a/BAlleleFreqFormat.py b/BAlleleFreqFormat.py index 09b6ef6..190a939 100644 --- a/BAlleleFreqFormat.py +++ b/BAlleleFreqFormat.py @@ -75,7 +75,6 @@ def generate_sample_format_info(self, bpm_records, vcf_record, sample_name): return "." for i in range(len(bpm_records)): snp = bpm_records[i].snp - print(snp) strand = bpm_records[i].ref_strand idx = bpm_records[i].index_num @@ -88,14 +87,13 @@ def generate_sample_format_info(self, bpm_records, vcf_record, sample_name): # normalize to reference allele ref_allele = vcf_record.REF + assert allele1 == ref_allele or allele2 == ref_allele # if allele1 is reference, then B allele is correct if allele1 == ref_allele: b_allele_freq_list.append(b_allele_freq) # if allele2 is reference, then we need to do 1-freq - elif allele2 == ref_allele: - b_allele_freq_list.append(1. - b_allele_freq) else: - print("ref allele: {} allele1: {} allele2: {}".format(ref_allele, allele1, allele2)) + b_allele_freq_list.append(1. - b_allele_freq) # nanmedian ignores NaN values final_b_allele_freq = np.nanmedian(b_allele_freq_list) diff --git a/gtc_to_vcf.py b/gtc_to_vcf.py index 46bc796..e06cc0a 100755 --- a/gtc_to_vcf.py +++ b/gtc_to_vcf.py @@ -72,6 +72,12 @@ def verify_inputs(args): return errors +def chrom_sort(chrom_string): + """ Convert input chromosome string to appropriate type to ensure native + sort functions sorts chromosomes in order 1-22,X,Y,MT + """ + return int(chrom_string) if str(chrom_string).isdigit() else chrom_string.lower() + def get_sample_name(gtc, gtc_file): sample_name = gtc.get_sample_name() if not sample_name: @@ -138,7 +144,7 @@ def driver(gtc_files, manifest_reader, genome_reader, output_vcf_files, expand_i format_factory = FormatFactory(gtc_files[0] is None, attrs_to_include, logger) reader_template_factory = ReaderTemplateFactory(genome_reader, format_factory, "4.1", "gtc_to_vcf " + VERSION, chrom_sort, logger) vcf_record_factory = VcfRecordFactory(format_factory, genome_reader, expand_identifiers, auxiliary_records, logger) - locus_entries = LocusEntryFactory(vcf_record_factory, genome_reader.get_contig_order(), unsquash_duplicates, logger).create_locus_entries(manifest_reader) + locus_entries = LocusEntryFactory(vcf_record_factory, chrom_sort, unsquash_duplicates, logger).create_locus_entries(manifest_reader) for (gtc_file, output_vcf_file) in zip(gtc_files, output_vcf_files): if gtc_file: From cae2df027d5c0de560f93a69d694e9425ff8c1d0 Mon Sep 17 00:00:00 2001 From: Jake Zieve Date: Thu, 9 May 2019 17:08:43 -0700 Subject: [PATCH 24/34] Update README with Include Attributes section --- README.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/README.md b/README.md index 53bcd97..6dee2e1 100644 --- a/README.md +++ b/README.md @@ -91,6 +91,11 @@ The GTC converter tool provides an option to supply a list of auxiliary records * The auxiliary definition must be a multi-nucleotide variant. * There must not be multiple array assays (e.g., duplicates) for the locus. +### Include Attributes +Default attributes to be included in the VCF are "GT" (genotype) and "GQ" (genotype score). +With this option, you can compose which fields from the GTC are output to the VCF. +The additional fields available (from GTC version 5) are "BAF" (B-Allele Frequency) and "LRR" (Log-R Ratio). + ## Output description The VCF file output follows VCF4.1 format (https://samtools.github.io/hts-specs/VCFv4.1.pdf). Some additional details on output formatting: * Genotypes are adjusted to reflect the sample ploidy. Calls are haploid for loci on Y, MT and non-PAR chromosome X for males. From 42191f42845236c24ff310ed64b5cd7021b5e34a Mon Sep 17 00:00:00 2001 From: Jake Zieve Date: Thu, 9 May 2019 17:55:07 -0700 Subject: [PATCH 25/34] Not sure where the chrom_sort function came from... --- gtc_to_vcf.py | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/gtc_to_vcf.py b/gtc_to_vcf.py index e06cc0a..f95f3ab 100755 --- a/gtc_to_vcf.py +++ b/gtc_to_vcf.py @@ -72,12 +72,6 @@ def verify_inputs(args): return errors -def chrom_sort(chrom_string): - """ Convert input chromosome string to appropriate type to ensure native - sort functions sorts chromosomes in order 1-22,X,Y,MT - """ - return int(chrom_string) if str(chrom_string).isdigit() else chrom_string.lower() - def get_sample_name(gtc, gtc_file): sample_name = gtc.get_sample_name() if not sample_name: @@ -142,9 +136,9 @@ def read_auxiliary_records(auxiliary_loci): def driver(gtc_files, manifest_reader, genome_reader, output_vcf_files, expand_identifiers, unsquash_duplicates, auxiliary_records, attrs_to_include, logger): format_factory = FormatFactory(gtc_files[0] is None, attrs_to_include, logger) - reader_template_factory = ReaderTemplateFactory(genome_reader, format_factory, "4.1", "gtc_to_vcf " + VERSION, chrom_sort, logger) + reader_template_factory = ReaderTemplateFactory(genome_reader, format_factory, "4.1", "gtc_to_vcf " + VERSION, genome_reader.get_contig_order(), logger) vcf_record_factory = VcfRecordFactory(format_factory, genome_reader, expand_identifiers, auxiliary_records, logger) - locus_entries = LocusEntryFactory(vcf_record_factory, chrom_sort, unsquash_duplicates, logger).create_locus_entries(manifest_reader) + locus_entries = LocusEntryFactory(vcf_record_factory, genome_reader.get_contig_order(), unsquash_duplicates, logger).create_locus_entries(manifest_reader) for (gtc_file, output_vcf_file) in zip(gtc_files, output_vcf_files): if gtc_file: From 1e13e1efa01b55dce9e24b6216dc826aeaf32414 Mon Sep 17 00:00:00 2001 From: Jake Zieve Date: Thu, 9 May 2019 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PASS . GT:GQ:BAF:LRR 0/0:0.470694:0.0375163555145:-0.302043 +1 3673329 newrs150537276 G T . PASS . GT:GQ:BAF:LRR 0/0:0.440959:0.000932812690735:0.0373033 +1 6592659 newrs146978611 G A . PASS . GT:GQ:BAF:LRR 0/0:0.459709:0.0:-0.0163632 +1 9083101 newrs148511942 G A . PASS . GT:GQ:BAF:LRR 0/0:0.517935:0.0:-0.468414 +1 11855351 newrs147750177 C A . PASS . GT:GQ:BAF:LRR 0/0:0.437521:0.0:0.0952104 +1 12815677 newrs147495703 C T . PASS . GT:GQ:BAF:LRR 0/0:0.416216:0.00122195482254:-0.00691045 +1 15886141 newrs148404423 C T . PASS . GT:GQ:BAF:LRR 0/0:0.507022:0.0:-0.134808 +1 17355095 newrs150542357 G A . PASS . GT:GQ:BAF:LRR 0/0:0.386914:0.0:-0.027109 +1 17606926 newrs148561129 T C . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.000139713:-0.216337 +1 23761066 newrs147652133 G A . PASS . GT:GQ:BAF:LRR 0/0:0.450165:0.0:0.0327107 +1 24706142 newrs149733917 C T . PASS . GT:GQ:BAF:LRR 0/0:0.495026:0.0:0.134454 +1 25569197 newrs149585550 C T . PASS . GT:GQ:BAF:LRR 0/0:0.518814:0.0:-0.0799513 +1 27210706 newrs149255985 G A . PASS . GT:GQ:BAF:LRR 0/0:0.518421:0.0:-0.00447297 +1 32686800 newrs146923152 T C . PASS . GT:GQ:BAF:LRR 0/0:0.400206:0.0:-0.0655664 +1 38005758 newrs150740046 C A . PASS . GT:GQ:BAF:LRR 0/0:0.422011:0.0:0.140212 +1 38041298 newrs148032409 G A . PASS . GT:GQ:BAF:LRR 0/0:0.458729:0.00232577323914:0.052806 +1 39824545 newrs148300193 G A . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.309027 +1 40546155 newrs148412181 C T . PASS . GT:GQ:BAF:LRR 0/0:0.361595:0.0:0.0901604 +1 40874410 newrs146684027 C T . PASS . GT:GQ:BAF:LRR 0/0:0.471341:0.0:0.154208 +1 40928587 newrs148910082 G T . PASS . GT:GQ:BAF:LRR 0/0:0.516679:0.0:0.136911 +1 41012572 newrs149604550 G T . PASS . GT:GQ:BAF:LRR 0/0:0.492112:0.0:-1.01427 +1 42671432 newrs148054297 C T . PASS . GT:GQ:BAF:LRR 0/0:0.517206:0.0:0.00124651 +1 43119487 newrs147914563 A C . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.268466 +1 44257821 newrs148531289 G A . PASS . GT:GQ:BAF:LRR 0/0:0.500078:0.0:0.0420391 +1 45479585 newrs150702733 C T . PASS . GT:GQ:BAF:LRR 0/0:0.487346:0.0120387077332:-0.117675 +1 46032360 newrs150476930 G A . PASS . GT:GQ:BAF:LRR 0/0:0.502872:0.0:0.182893 +1 47101568 newrs149829714 C A . PASS . GT:GQ:BAF:LRR 0/0:0.411203:0.0:0.0375702 +1 47149049 newrs149160356 G T . PASS . GT:GQ:BAF:LRR 0/0:0.468272:0.0:-0.0719191 +1 47571800 newrs149156333 G A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:-0.0608993 +1 48771458 newrs150721160 C A . PASS . GT:GQ:BAF:LRR 0/0:0.511883:0.0:0.332273 +1 53153451 newrs149085843 G A . PASS . GT:GQ:BAF:LRR 0/0:0.336045:0.00500947237015:-0.0643592 +1 55277538 newrs148698352 G A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.161932 +1 55307307 newrs147428017 G A . PASS . GT:GQ:BAF:LRR 0/0:0.467145:0.0:0.0115098 +1 57207829 newrs148260034 C T . PASS . GT:GQ:BAF:LRR 0/0:0.516963:0.0:-0.0790384 +1 57422472 newrs150022116 G A . PASS . GT:GQ:BAF:LRR 0/0:0.403158:0.0:0.0673411 +1 57610963 newrs148293352 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.00695061683655:0.132613 +1 60373471 newrs150250306 G T . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.0800018 +1 70761813 newrs150473953 T C . PASS . GT:GQ:BAF:LRR 0/0:0.510061:0.0:0.0189942 +1 76205797 newrs148260275 T C . PASS . GT:GQ:BAF:LRR 0/0:0.501148:0.0:-0.655021 +1 76211574 newrs149678400 C A . PASS . GT:GQ:BAF:LRR 0/0:0.516476:0.00524163246155:0.097089 +1 76226906 newrs148207467 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500204:0.0024516582489:-0.302519 +1 76226946 newrs150310121 G A . PASS . GT:GQ:BAF:LRR 0/0:0.517069:0.0:0.176186 +1 79094069 newrs147126504 C T . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.00148546695709:-0.410639 +1 85431301 newrs148979230 G T . PASS . GT:GQ:BAF:LRR 0/0:0.510376:0.0:0.0263765 +1 89520397 newrs150057659 C A . PASS . GT:GQ:BAF:LRR 0/0:0.517815:0.0157161951065:-0.385665 +1 89616216 newrs150032762 C T . PASS . GT:GQ:BAF:LRR 0/0:0.489807:0.0:0.0995271 +1 89734412 newrs147816214 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.0986295 +1 90478723 newrs149719190 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500107:0.000285029411316:-0.0801836 +1 94578619 newrs150452677 G A . PASS . GT:GQ:BAF:LRR 0/0:0.376958:0.0:-0.0854469 +1 97915724 newrs147601618 A G . PASS . GT:GQ:BAF:LRR 0/0:0.467283:0.000459123:0.0661342 +1 108697712 newrs147531188 G A . PASS . GT:GQ:BAF:LRR 0/0:0.49223:0.0:-0.390987 +1 109315442 newrs148829120 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519554:0.0:-0.134188 +1 109358861 newrs149826017 G A . PASS . GT:GQ:BAF:LRR 0/0:0.517514:0.0:0.0669972 +1 110280079 newrs149969876 C T . PASS . GT:GQ:BAF:LRR 0/0:0.494467:0.0:-0.353095 +1 111783947 newrs149638402 A C . PASS . GT:GQ:BAF:LRR 0/0:0.471613:0.0:-0.0765495 +1 112020623 newrs147652304 G T . PASS . GT:GQ:BAF:LRR 0/0:0.399274:0.0:0.0895069 +1 113253230 newrs147305772 G A . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.000909924507141:0.200122 +1 114443858 newrs149705131 C T . PASS . GT:GQ:BAF:LRR 0/0:0.508243:0.0:0.0274177 +1 114450747 newrs150374247 C T . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:0.0562876 +1 114641717 newrs149899868 G A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0370052456856:0.0423265 +1 117620549 newrs150482379 C T . PASS . GT:GQ:BAF:LRR 0/0:0.495602:0.0:0.100861 +1 118494704 newrs149832695 G A . PASS . GT:GQ:BAF:LRR 0/0:0.443041:0.0:0.174005 +1 120277390 newrs149128100 G A . PASS . GT:GQ:BAF:LRR 0/0:0.469331:0.0404487848282:-0.265325 +1 146765310 newrs149664186 C T . PASS . GT:GQ:BAF:LRR 0/0:0.374745:0.0:0.016838 +1 150236277 newrs150286906 G A . PASS . GT:GQ:BAF:LRR 0/0:0.454041:0.0:0.190005 +1 150679139 newrs150156011 G A . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:-0.192496 +1 150680779 newrs147466313 A C . PASS . GT:GQ:BAF:LRR 0/0:0.470807:0.0:-0.234179 +1 150935195 newrs148336558 T C . PASS . GT:GQ:BAF:LRR 0/0:0.450795:0.0:-0.0358204 +1 151774172 newrs149393439 G A . PASS . GT:GQ:BAF:LRR 0/0:0.498079:0.0:0.302621 +1 152323551 newrs150581091 A C . PASS . GT:GQ:BAF:LRR 0/0:0.49567:0.0:-0.191636 +1 152325692 newrs148445702 G A . PASS . GT:GQ:BAF:LRR 0/0:0.483939:0.00202637910843:0.125953 +1 152882541 newrs149812110 C T . PASS . GT:GQ:BAF:LRR 0/0:0.468768:0.0:-0.152137 +1 154247447 newrs149409924 G A . PASS . GT:GQ:BAF:LRR 0/0:0.487384:0.0:0.0326374 +1 154956201 newrs149321878 C T . PASS . GT:GQ:BAF:LRR 0/0:0.441128:0.0:0.105524 +1 155001836 newrs149078228 G T . PASS . GT:GQ:BAF:LRR 0/0:0.496628:0.0:-0.277777 +1 155170349 newrs147564978 G T . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.0:0.0712592 +1 155686919 newrs148684040 G A . PASS . GT:GQ:BAF:LRR 0/0:0.518594:0.0:-0.227205 +1 156316558 newrs150769956 G A . PASS . GT:GQ:BAF:LRR 0/0:0.469558:0.0:-0.058503 +1 156563199 newrs147197432 G A . PASS . GT:GQ:BAF:LRR 0/0:0.505226:0.00189685821533:-0.681026 +1 156641687 newrs148343241 G A . PASS . GT:GQ:BAF:LRR 0/0:0.514253:0.0:-0.522988 +1 158151902 newrs149673076 C T . PASS . GT:GQ:BAF:LRR 0/0:0.898959:0.0:0.0407713 +1 158912073 newrs150672460 C T . PASS . GT:GQ:BAF:LRR 0/0:0.464363:0.0170405507088:-0.459974 +1 159779984 newrs148078638 T G . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.0473273 +1 160169695 newrs150143470 G T . PASS . GT:GQ:BAF:LRR 0/0:0.402652:0.0114940404892:0.105376 +1 160850944 newrs148939374 C A . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:0.0947338 +1 161475798 newrs148134119 G T . PASS . GT:GQ:BAF:LRR 0/0:0.49429:0.0106179714203:-0.0252612 +1 165664632 newrs146792904 G A . PASS . GT:GQ:BAF:LRR 0/0:0.496135:0.0:0.0620832 +1 167042622 newrs148369513 C T . PASS . GT:GQ:BAF:LRR 0/0:0.453531:0.0:-0.0277512 +1 169256540 newrs146620013 C T . PASS . GT:GQ:BAF:LRR 0/0:0.50859:0.0:0.0997077 +1 171753321 newrs150322704 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500095:0.000733256340027:-0.118102 +1 173807353 newrs149035108 C T . PASS . GT:GQ:BAF:LRR 0/0:0.513198:0.0:0.0379539 +1 175325455 newrs146606650 G A . PASS . GT:GQ:BAF:LRR 0/0:0.361595:0.0:-0.0997824 +1 179052127 newrs149563285 G A . PASS . GT:GQ:BAF:LRR 0/0:0.493009:0.0230234861374:0.00378964 +1 179307032 newrs148646476 G T . PASS . GT:GQ:BAF:LRR 0/0:0.505716:0.0:0.0549275 +1 179354442 newrs149782250 C T . PASS . GT:GQ:BAF:LRR 0/0:0.495637:0.0:-0.22645 +1 179363138 newrs148772825 G T . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:-0.045627 +1 183194742 newrs149195906 G A . PASS . GT:GQ:BAF:LRR 0/0:0.510512:0.0:-0.650326 +1 185833761 newrs149911074 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0011528134346:0.0138784 +1 186084057 newrs150673369 C T . PASS . GT:GQ:BAF:LRR 0/0:0.489922:0.0:0.073639 +1 186281504 newrs150684195 G A . PASS . GT:GQ:BAF:LRR 0/0:0.518561:0.0:0.167807 +1 196227323 newrs148932019 C T . PASS . GT:GQ:BAF:LRR 0/0:0.419087:0.0:0.119276 +1 196694379 newrs148165372 G A . PASS . GT:GQ:BAF:LRR 0/0:0.897186:0.0:-0.212459 +1 197073245 newrs148294838 G T . PASS . GT:GQ:BAF:LRR 0/0:0.348161:0.0:0.0820793 +1 201972364 newrs149489527 G T . PASS . GT:GQ:BAF:LRR 0/0:0.402445:0.0:-0.087078 +1 202302658 newrs149154798 G A . PASS . GT:GQ:BAF:LRR 0/0:0.51072:0.0:-0.0265459 +1 205053076 newrs148879722 G A . PASS . GT:GQ:BAF:LRR 0/0:0.430531:0.0:-0.019981 +1 207963618 newrs146803767 C T . PASS . GT:GQ:BAF:LRR 0/0:0.507719:0.0:0.0164705 +1 210536268 newrs149074859 A C . PASS . GT:GQ:BAF:LRR 0/0:0.420059:0.0:0.0323695 +1 211842488 newrs146817802 G A . PASS . GT:GQ:BAF:LRR 0/0:0.502779:0.0210029482841:-0.98664 +1 212911789 newrs150149847 C T . PASS . GT:GQ:BAF:LRR 0/0:0.518952:0.0:0.0199789 +1 215814065 newrs146733615 G A . PASS . GT:GQ:BAF:LRR 0/0:0.456784:0.0:0.0486638 +1 217671697 newrs148242273 C A . PASS . GT:GQ:BAF:LRR 0/0:0.474365:0.0:0.00974765 +1 220157548 newrs148272159 C T . PASS . GT:GQ:BAF:LRR 0/0:0.506557:0.0:-0.432919 +1 223176941 newrs147375741 C A . PASS . GT:GQ:BAF:LRR 0/0:0.420376:0.00432181358337:-0.0499767 +1 230895268 newrs146559174 G A . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:0.0876401 +1 235577747 newrs148321184 G A . PASS . GT:GQ:BAF:LRR ./.:0.0787613:0.2217643857:-0.0767733 +1 235647638 newrs146580273 C T . PASS . GT:GQ:BAF:LRR 0/0:0.512115:0.0:0.0819448 +1 237037078 newrs147387989 T C . PASS . GT:GQ:BAF:LRR 0/0:0.514123:0.0:-0.051399 +1 237711862 newrs149514924 G A . PASS . GT:GQ:BAF:LRR 0/0:0.759267:0.0:-0.231418 +1 247614403 newrs148864378 G T . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0133163928986:-0.00174375 +2 272247 newrs148640616 C T . PASS . GT:GQ:BAF:LRR 0/0:0.490533:0.0113739967346:-0.251815 +2 21232203 newrs146538280 G A . PASS . GT:GQ:BAF:LRR 0/0:0.486666:0.0:-0.20968 +2 21233706 newrs147863759 G A . PASS . GT:GQ:BAF:LRR 0/0:0.419284:0.00512051582336:0.0625729 +2 25013405 newrs150693486 G A . PASS . GT:GQ:BAF:LRR 0/0:0.402255:0.0:0.0949489 +2 25022714 newrs147240609 G A . PASS . GT:GQ:BAF:LRR 0/0:0.418876:0.00519400835037:0.100752 +2 25179912 newrs150189609 C T . PASS . GT:GQ:BAF:LRR 0/0:0.514077:0.0:-0.119383 +2 25190147 newrs147784881 G A . PASS . GT:GQ:BAF:LRR 0/0:0.473966:0.0:0.0965744 +2 27522267 newrs147280617 A G . PASS . GT:GQ:BAF:LRR 0/0:0.514545:0.0105097:-0.131562 +2 27702472 newrs150619589 C T . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0127893686295:0.0691737 +2 27726415 newrs149847328 C T . PASS . GT:GQ:BAF:LRR 0/0:0.516143:0.0:-0.139037 +2 27891739 newrs147763001 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:0.0355234 +2 28754975 newrs146560841 C T . PASS . GT:GQ:BAF:LRR 0/0:0.512898:0.0:-0.27977 +2 32477660 newrs148696946 C T . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.0662636 +2 33526713 newrs149091174 T G . PASS . GT:GQ:BAF:LRR 0/0:0.51335:0.0:-0.103584 +2 33749620 newrs147803655 A G . PASS . GT:GQ:BAF:LRR 0/0:0.822063:0.0:-0.00385946 +2 37010481 newrs147643782 A G . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.0660986 +2 37264998 newrs148649473 A G . PASS . GT:GQ:BAF:LRR 0/0:0.48068:0.0:-0.879975 +2 37406712 newrs147099571 G A . PASS . GT:GQ:BAF:LRR 0/0:0.496967:0.0:-0.183926 +2 39509654 newrs150038225 A G . PASS . GT:GQ:BAF:LRR 0/0:0.499933:0.0:0.00634611 +2 44010657 newrs148986857 A C . PASS . GT:GQ:BAF:LRR 0/0:0.498598:0.0:-0.354151 +2 44993596 newrs148200193 C T . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:-0.27766 +2 45620111 newrs148978058 G A . PASS . GT:GQ:BAF:LRR 0/0:0.456094:0.0:0.0208677 +2 45807089 newrs149253392 C A . PASS . GT:GQ:BAF:LRR 0/0:0.498831:0.0:-0.242171 +2 47637347 newrs149511545 G A . PASS . GT:GQ:BAF:LRR 0/0:0.511852:0.0:0.00770109 +2 48686892 newrs146977827 G A . PASS . GT:GQ:BAF:LRR 0/0:0.510909:0.00953328609467:-0.227503 +2 48950760 newrs150650490 C T . PASS . GT:GQ:BAF:LRR 0/0:0.511852:0.00571292638779:0.00218081 +2 54081194 newrs148952285 G A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:-0.0998538 +2 61411935 newrs148994739 G A . PASS . GT:GQ:BAF:LRR 0/0:0.517442:0.0:-0.0867382 +2 63058153 newrs150648830 G A . PASS . GT:GQ:BAF:LRR 0/0:0.511325:0.0:0.0589336 +2 69297862 newrs148248879 T C . PASS . GT:GQ:BAF:LRR 0/0:0.484905:0.0143264:-0.727175 +2 71351536 newrs147401037 T G . PASS . GT:GQ:BAF:LRR 0/0:0.511852:0.0:-0.334952 +2 73635852 newrs150825781 C T . PASS . GT:GQ:BAF:LRR 0/0:0.86255:0.0:-0.0263483 +2 74450060 newrs148722557 G T . PASS . GT:GQ:BAF:LRR 0/0:0.409735:0.0:0.0999527 +2 74750267 newrs150420269 G A . PASS . GT:GQ:BAF:LRR 0/0:0.51373:0.0:-0.148445 +2 79254997 newrs147143164 G A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:-0.00317882 +2 86677062 newrs150111816 C T . PASS . GT:GQ:BAF:LRR 0/0:0.516018:0.0:-0.306152 +2 98986540 newrs147118493 G A . PASS . GT:GQ:BAF:LRR 0/0:0.399199:0.000653743743896:0.0994308 +2 99012315 newrs147415641 G A . PASS . GT:GQ:BAF:LRR 0/0:0.491018:0.0:-0.034182 +2 99634774 newrs146845080 G T . PASS . GT:GQ:BAF:LRR 0/0:0.364964:0.0:-0.130241 +2 103335503 newrs150229633 C T . PASS . GT:GQ:BAF:LRR 0/0:0.457166:0.0:-0.47163 +2 113330180 newrs148462768 C T . PASS . GT:GQ:BAF:LRR 0/0:0.49091:0.0:-0.0910289 +2 135745136 newrs147939837 C A . PASS . GT:GQ:BAF:LRR 0/0:0.507462:0.0:0.162704 +2 136558283 newrs146614143 C T . PASS . GT:GQ:BAF:LRR 0/0:0.511644:0.0:0.0188863 +2 141259256 newrs149427515 C A . PASS . GT:GQ:BAF:LRR 0/0:0.510475:0.0:0.212941 +2 153415337 newrs148249353 C T . PASS . GT:GQ:BAF:LRR 0/0:0.49181:0.0118697881699:-0.238699 +2 158977989 newrs148797309 C T . PASS . GT:GQ:BAF:LRR 0/0:0.510234:0.0051736831665:-0.432319 +2 160697239 newrs149752222 C T . PASS . GT:GQ:BAF:LRR 0/0:0.495101:0.00832676887512:0.0413836 +2 160826719 newrs146991124 G T . PASS . GT:GQ:BAF:LRR 0/0:0.495752:0.0:0.141565 +2 170387132 newrs148187838 G A . PASS . GT:GQ:BAF:LRR 0/0:0.498764:0.0:-0.714172 +2 171715408 newrs147201199 G A . PASS . GT:GQ:BAF:LRR 0/0:0.499822:0.0:-0.461191 +2 173352274 newrs148112672 G A . PASS . GT:GQ:BAF:LRR 0/0:0.485714:0.0:-0.00548074 +2 174231932 newrs150220964 C T . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:0.080326 +2 179602841 newrs147879266 C T . PASS . GT:GQ:BAF:LRR 0/0:0.889129:0.0:-0.184389 +2 179632509 newrs146572907 G A . PASS . GT:GQ:BAF:LRR 0/0:0.518824:0.0:0.0425156 +2 182468660 newrs147234433 C A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.00178442 +2 187626443 newrs149426133 C T . PASS . GT:GQ:BAF:LRR 0/0:0.517635:0.0:-0.160677 +2 189861949 newrs146652498 G A . PASS . GT:GQ:BAF:LRR 0/0:0.894299:0.0:0.0337128 +2 189872776 newrs147706051 A G . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.133614 +2 189948710 newrs150092345 C T . PASS . GT:GQ:BAF:LRR 0/0:0.312364:0.0138638019562:0.0751853 +2 190728842 newrs148214055 G T . PASS . GT:GQ:BAF:LRR 0/0:0.503287:0.0:-0.0496794 +2 197143252 newrs148753553 C T . PASS . GT:GQ:BAF:LRR 0/0:0.430166:0.00457906723022:-0.373217 +2 198011817 newrs147529433 G A . PASS . GT:GQ:BAF:LRR 0/0:0.511407:0.0:0.102923 +2 201468080 newrs148871699 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.0827931 +2 201485454 newrs148848561 G T . PASS . GT:GQ:BAF:LRR 0/0:0.514503:0.0:-0.0231242 +2 201746205 newrs148778524 C T . PASS . GT:GQ:BAF:LRR 0/0:0.458434:0.0:-0.254425 +2 202139656 newrs146816437 G T . PASS . GT:GQ:BAF:LRR 0/0:0.480718:0.0:-0.98259 +2 211481201 newrs147062907 A G . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.0480907 +2 213872794 newrs146574423 G A . PASS . GT:GQ:BAF:LRR 0/0:0.516934:0.0:0.0531858 +2 214161989 newrs147302970 C A . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.00729429721832:0.13887 +2 215595159 newrs147215925 T C . PASS . GT:GQ:BAF:LRR 0/0:0.799495:0.0:-0.0562691 +2 219141726 newrs150313254 C T . PASS . GT:GQ:BAF:LRR 0/0:0.508287:0.0:0.10109 +2 220045436 newrs150059479 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.124957 +2 220285366 newrs146755676 G A . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:-0.00476619 +2 224463265 newrs149795847 C T . PASS . GT:GQ:BAF:LRR 0/0:0.371617:0.0:0.0363237 +2 224831713 newrs149165411 G T . PASS . GT:GQ:BAF:LRR 0/0:0.508769:0.0:-0.091282 +2 233625195 newrs149250246 G T . PASS . GT:GQ:BAF:LRR 0/0:0.388034:0.0:0.0264922 +2 234590826 newrs149618508 C A . PASS . GT:GQ:BAF:LRR 0/0:0.280187:0.012552022934:0.132973 +3 9426235 newrs149283084 C T . PASS . GT:GQ:BAF:LRR 0/0:0.481868:0.00136929750443:0.157917 +3 10136006 newrs148471911 C T . PASS . GT:GQ:BAF:LRR 0/0:0.487384:0.0247240066528:-0.0304888 +3 10953879 newrs149375519 G A . PASS . GT:GQ:BAF:LRR 0/0:0.516017:0.0:0.0202665 +3 12560697 newrs149417061 G A . PASS . GT:GQ:BAF:LRR 0/0:0.512616:0.00385147333145:0.0207241 +3 12791254 newrs149474579 C T . PASS . GT:GQ:BAF:LRR 0/0:0.509778:0.0:0.0885353 +3 14174410 newrs147336367 C T . PASS . GT:GQ:BAF:LRR 0/0:0.435188:0.0:-0.173993 +3 14745899 newrs146642906 C T . PASS . GT:GQ:BAF:LRR 0/0:0.711028:0.020172894001:-0.126525 +3 15288911 newrs149691332 C A . PASS . GT:GQ:BAF:LRR 0/0:0.373656:0.0624018907547:-0.281421 +3 15686732 newrs146600671 G A . PASS . GT:GQ:BAF:LRR 0/0:0.497704:0.0:-0.166274 +3 21706378 newrs147583836 C T . PASS . GT:GQ:BAF:LRR 0/0:0.529052:0.0:-0.0763009 +3 32801063 newrs146801343 A C . PASS . GT:GQ:BAF:LRR 0/0:0.528879:0.0:0.152315 +3 37150133 newrs149602102 G A . PASS . GT:GQ:BAF:LRR 0/0:0.506383:0.0112701654434:-0.0832593 +3 38053166 newrs148984703 T G . PASS . GT:GQ:BAF:LRR 0/0:0.483202:0.0:0.0454614 +3 38061820 newrs148796522 G A . PASS . GT:GQ:BAF:LRR 0/0:0.468348:0.0424809455872:-0.235997 +3 38307727 newrs147778100 G T . PASS . GT:GQ:BAF:LRR 0/0:0.513792:0.000425398349762:0.14366 +3 38739163 newrs149504103 G A . PASS . GT:GQ:BAF:LRR 0/0:0.50834:0.0:0.0647812 +3 38966906 newrs146942592 G A . PASS . GT:GQ:BAF:LRR 0/0:0.513848:0.0:-0.110957 +3 39178003 newrs148431487 G T . PASS . GT:GQ:BAF:LRR 0/0:0.512985:0.0:0.0317934 +3 40353062 newrs147698288 G A . PASS . GT:GQ:BAF:LRR 0/0:0.502759:0.0:0.00390594 +3 42955929 newrs147863526 G T . PASS . GT:GQ:BAF:LRR 0/0:0.515244:0.00456595420837:0.0228084 +3 44701410 newrs148645131 C T . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:0.0124902 +3 44762610 newrs146541622 G T . PASS . GT:GQ:BAF:LRR 0/0:0.512367:2.14576721191e-06:0.0573141 +3 44932143 newrs148772351 C T . PASS . GT:GQ:BAF:LRR 0/0:0.462291:0.0:0.135343 +3 46415393 newrs147879075 C T . PASS . GT:GQ:BAF:LRR 0/0:0.49784:0.0107857584953:-0.689954 +3 46479574 newrs150670421 A C . PASS . GT:GQ:BAF:LRR 0/0:0.374745:0.0:0.0508686 +3 48215773 newrs149350315 C A . PASS . GT:GQ:BAF:LRR 0/0:0.51022:0.0:0.160297 +3 49318198 newrs150287339 C A . PASS . GT:GQ:BAF:LRR 0/0:0.399452:0.0:0.172546 +3 52786032 newrs146877089 C T . PASS . GT:GQ:BAF:LRR 0/0:0.49897:0.0137360095978:-0.468127 +3 53886024 newrs149538576 A C . PASS . GT:GQ:BAF:LRR 0/0:0.289345:0.0:0.0668447 +3 56601067 newrs149475199 G A . PASS . GT:GQ:BAF:LRR 0/0:0.487683:0.0:0.039046 +3 58494643 newrs147680655 G A . PASS . GT:GQ:BAF:LRR 0/0:0.499881:0.0:0.0510018 +3 58519760 newrs149540578 G A . PASS . GT:GQ:BAF:LRR 0/0:0.376958:0.0:0.0841575 +3 69988298 newrs149249176 G A . PASS . GT:GQ:BAF:LRR 0/0:0.49553:0.0:0.0267149 +3 71748775 newrs149437626 G A . PASS . GT:GQ:BAF:LRR 0/0:0.513289:0.0:-0.23323 +3 73657837 newrs149396248 T G . PASS . GT:GQ:BAF:LRR 0/0:0.48671:0.0:-0.0723483 +3 107497349 newrs150437555 C T . PASS . GT:GQ:BAF:LRR 0/0:0.459837:0.0:0.0404126 +3 107510124 newrs149104597 G A . PASS . GT:GQ:BAF:LRR 0/0:0.500553:0.0:-0.299453 +3 109027122 newrs150350350 G A . PASS . GT:GQ:BAF:LRR 0/0:0.413243:0.00371915102005:-0.0767541 +3 109052769 newrs150133131 T C . PASS . GT:GQ:BAF:LRR 0/0:0.420089:0.0:-0.0862267 +3 111343251 newrs150804090 T C . PASS . GT:GQ:BAF:LRR 0/0:0.511852:0.0:-0.117912 +3 111799851 newrs147783135 C T . PASS . GT:GQ:BAF:LRR 0/0:0.487442:0.0:-0.37333 +3 113286557 newrs148646920 G A . PASS . GT:GQ:BAF:LRR 0/0:0.500101:0.0:0.00803275 +3 113335009 newrs150137878 C T . PASS . GT:GQ:BAF:LRR 0/0:0.478579:0.0:-0.0937002 +3 119211127 newrs150029976 A C . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.0675809 +3 119325752 newrs148143400 G T . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.0125678 +3 119434591 newrs147597066 G A . PASS . GT:GQ:BAF:LRR 0/0:0.512854:0.0:0.139649 +3 121202346 newrs150312701 G A . PASS . GT:GQ:BAF:LRR 0/0:0.503841:0.00116169452667:-0.197379 +3 121345582 newrs149561440 G A . PASS . GT:GQ:BAF:LRR 0/0:0.374745:0.0255137085915:0.018823 +3 121658264 newrs148008499 G A . PASS . GT:GQ:BAF:LRR 0/0:0.495217:0.0:-0.157029 +3 122487730 newrs150320476 C A . PASS . GT:GQ:BAF:LRR 0/0:0.508439:0.0:-0.154177 +3 125188298 newrs150435491 A G . PASS . GT:GQ:BAF:LRR 0/0:0.500145:0.0:-0.0860629 +3 128612406 newrs148694290 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500042:0.0:-0.718188 +3 130282510 newrs150427289 T C . PASS . GT:GQ:BAF:LRR 0/0:0.828074:0.0:-0.136943 +3 130871352 newrs150253539 T G . PASS . GT:GQ:BAF:LRR 0/0:0.438791:0.0:0.329487 +3 132036382 newrs149109145 C T . PASS . GT:GQ:BAF:LRR 0/0:0.517813:0.0:-0.211665 +3 132400757 newrs147332157 C T . PASS . GT:GQ:BAF:LRR 0/0:0.516853:0.0:0.0418239 +3 132407950 newrs148670389 G A . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:0.120365 +3 133473346 newrs150548621 G A . PASS . GT:GQ:BAF:LRR 0/0:0.51048:0.0:-0.0776137 +3 133553479 newrs147187493 G A . PASS . GT:GQ:BAF:LRR 0/0:0.497686:0.0:-0.650794 +3 137886048 newrs149610079 G A . PASS . GT:GQ:BAF:LRR 0/0:0.514725:0.0:-0.192194 +3 138248217 newrs146572731 C T . PASS . GT:GQ:BAF:LRR 0/0:0.499361:0.0:0.165248 +3 141626116 newrs149224279 C T . PASS . GT:GQ:BAF:LRR 0/0:0.517493:0.0:0.0157167 +3 142408660 newrs148218811 G A . PASS . GT:GQ:BAF:LRR 0/0:0.322583:0.0:-0.0247877 +3 148459591 newrs150330554 C T . PASS . GT:GQ:BAF:LRR 0/0:0.387978:0.0:-0.0471387 +3 148759953 newrs149074331 C T . PASS . GT:GQ:BAF:LRR 0/0:0.458472:0.0:0.129733 +3 150931294 newrs148423792 C A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.081865 +3 151538170 newrs150063056 G A . PASS . GT:GQ:BAF:LRR 0/0:0.512231:0.0:-0.0150575 +3 154802023 newrs150836510 C T . PASS . GT:GQ:BAF:LRR 0/0:0.507578:0.0:-0.565702 +3 154862172 newrs149905705 C T . PASS . GT:GQ:BAF:LRR 0/0:0.514676:0.0:-0.290743 +3 160156268 newrs150089676 A C . PASS . GT:GQ:BAF:LRR 0/0:0.498265:0.0:0.0487368 +3 165548629 newrs148170012 G A . PASS . GT:GQ:BAF:LRR 0/0:0.501483:0.0:-0.219884 +3 167159974 newrs148696355 C T . PASS . GT:GQ:BAF:LRR 0/0:0.503189:0.0:0.0689014 +3 167189391 newrs150619093 G A . PASS . GT:GQ:BAF:LRR 0/0:0.481547:0.0:0.0828095 +3 169511489 newrs146621484 A C . PASS . GT:GQ:BAF:LRR 0/0:0.483108:0.0:0.138287 +3 172482204 newrs148663230 G A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.121419 +3 172634118 newrs146640459 C A . PASS . GT:GQ:BAF:LRR 0/0:0.511852:0.0:0.173031 +3 172674467 newrs149140561 C T . PASS . GT:GQ:BAF:LRR 0/0:0.484945:0.00206476449966:0.14995 +3 183211920 newrs147068041 G A . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:0.00196975 +3 184922543 newrs146633671 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.0319869 +3 185879392 newrs149298788 C T . PASS . GT:GQ:BAF:LRR 0/0:0.437916:0.0:-0.0617891 +3 186289915 newrs148976481 C T . PASS . GT:GQ:BAF:LRR 0/0:0.465095:0.0:-0.0633064 +3 186510326 newrs150799698 G A . PASS . GT:GQ:BAF:LRR 0/0:0.511468:0.0:-0.137579 +3 186510593 newrs147162624 C T . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.175528 +3 186940950 newrs148556944 G A . PASS . GT:GQ:BAF:LRR 0/0:0.443245:0.00648820400238:0.038031 +3 192973578 newrs149064282 G A . PASS . GT:GQ:BAF:LRR 0/0:0.505164:0.0127172470093:-0.531173 +3 193036880 newrs148097145 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.131214 +3 193365922 newrs147077380 G A . PASS . GT:GQ:BAF:LRR 0/0:0.475612:0.0:0.0377081 +3 194313800 newrs150713705 C T . PASS . GT:GQ:BAF:LRR 0/0:0.499083:0.00878554582596:0.105485 +3 195785154 newrs147330019 C T . PASS . GT:GQ:BAF:LRR 0/0:0.478774:0.0:0.00708426 +3 196214335 newrs148275050 G A . PASS . GT:GQ:BAF:LRR 0/0:0.39725:0.0:-0.154492 +3 196281651 newrs150731771 G A . PASS . GT:GQ:BAF:LRR 0/0:0.351044:0.0:0.154451 +4 366855 newrs147483014 G A . PASS . GT:GQ:BAF:LRR 0/0:0.263285:0.0:0.00338186 +4 844776 newrs149731617 G A . PASS . GT:GQ:BAF:LRR 0/0:0.509334:0.0:0.105907 +4 890248 newrs149963126 C T . PASS . GT:GQ:BAF:LRR 0/0:0.497629:0.0:-0.0712523 +4 2948210 newrs150411289 G A . PASS . GT:GQ:BAF:LRR 0/0:0.354281:0.0459765195847:-0.329292 +4 4322933 newrs148926395 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:0.141315 +4 8383293 newrs146945288 G A . PASS . GT:GQ:BAF:LRR 0/0:0.502229:0.0:-0.102048 +4 8467193 newrs147229355 C T . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.0884682 +4 36345134 newrs149895631 G A . PASS . GT:GQ:BAF:LRR 0/0:0.758343:0.0:-0.0648703 +4 40144398 newrs149506250 C T . PASS . GT:GQ:BAF:LRR 0/0:0.471953:0.0:0.0939122 +4 48037577 newrs148207193 A G . PASS . GT:GQ:BAF:LRR 0/0:0.509715:0.0:-0.036752 +4 48852065 newrs148329796 C T . PASS . GT:GQ:BAF:LRR 0/0:0.499734:0.0:-0.228192 +4 48993509 newrs149499062 C T . PASS . GT:GQ:BAF:LRR 0/0:0.502054:0.0:-0.100949 +4 52895932 newrs150518260 G A . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:0.153992 +4 57215500 newrs149271822 C T . PASS . GT:GQ:BAF:LRR 0/0:0.473282:0.0:-0.0322665 +4 68447022 newrs147302126 G A . PASS . GT:GQ:BAF:LRR 0/0:0.422059:0.0:-0.196124 +4 68606388 newrs148499544 A C . PASS . GT:GQ:BAF:LRR 0/0:0.519131:0.0:-0.137615 +4 68938040 newrs148214799 C T . PASS . GT:GQ:BAF:LRR 0/0:0.487435:0.0:0.228372 +4 69342156 newrs147196017 C T . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.0483638 +4 70596214 newrs148007908 T G . PASS . GT:GQ:BAF:LRR 0/0:0.514785:0.0:0.146563 +4 71507790 newrs146706831 C T . PASS . GT:GQ:BAF:LRR 0/0:0.497783:0.00540226697922:-0.0569451 +4 71670135 newrs147166750 T C . PASS . GT:GQ:BAF:LRR 0/0:0.432716:0.0:0.0936925 +4 73178008 newrs146827790 G A . PASS . GT:GQ:BAF:LRR 0/0:0.322395:0.0:-0.246146 +4 73184295 newrs150704470 G T . PASS . GT:GQ:BAF:LRR 0/0:0.498366:0.0:-0.364079 +4 74284028 newrs149079814 C T . PASS . GT:GQ:BAF:LRR 0/0:0.501102:0.011549949646:-0.388384 +4 74365763 newrs147051358 C T . PASS . GT:GQ:BAF:LRR 0/0:0.344362:0.0:-0.0723751 +4 76489574 newrs146645381 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.0526185 +4 89671574 newrs148165624 C A . PASS . GT:GQ:BAF:LRR 0/0:0.487661:0.0:-0.128073 +4 90844405 newrs146692577 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500204:0.00161904096603:0.199314 +4 98865046 newrs150178155 A G . PASS . GT:GQ:BAF:LRR 0/0:0.514402:0.0:-0.0980106 +4 100826754 newrs149618769 G A . PASS . GT:GQ:BAF:LRR 0/0:0.233143:0.0699843168259:-0.0372861 +4 109667672 newrs146606272 G A . PASS . GT:GQ:BAF:LRR 0/0:0.487384:0.0:-0.00448393 +4 110617569 newrs148210591 C A . PASS . GT:GQ:BAF:LRR 0/0:0.481828:0.0:0.132258 +4 111474579 newrs148232326 G A . PASS . GT:GQ:BAF:LRR 0/0:0.509057:0.00473064184189:0.193807 +4 114430793 newrs148603207 C T . PASS . GT:GQ:BAF:LRR 0/0:0.510791:0.0:0.0720721 +4 119239531 newrs149455950 A G . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.0354826 +4 122593688 newrs146935113 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.0914721 +4 122593712 newrs147110745 G A . PASS . GT:GQ:BAF:LRR 0/0:0.503454:0.0:-0.0155689 +4 122682805 newrs148344547 G A . PASS . GT:GQ:BAF:LRR 0/0:0.499527:0.00511652231216:0.0971537 +4 123868644 newrs149688478 G A . PASS . GT:GQ:BAF:LRR 0/0:0.504149:0.0:-0.237321 +4 126408554 newrs148483308 G T . PASS . GT:GQ:BAF:LRR 0/0:0.497407:0.0:-0.217825 +4 128859937 newrs148601655 C A . PASS . GT:GQ:BAF:LRR 0/0:0.509562:0.0:-0.260451 +4 141484263 newrs147778681 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500305:0.0:0.045705 +4 148800491 newrs150075964 T G . PASS . GT:GQ:BAF:LRR 0/0:0.409735:0.0:-0.199415 +4 164393674 newrs148025040 G A . PASS . GT:GQ:BAF:LRR 0/0:0.480375:0.0:-0.0182719 +4 169085406 newrs147539910 G T . PASS . GT:GQ:BAF:LRR 0/0:0.518436:0.0:0.0309299 +4 169183151 newrs148697677 C T . PASS . GT:GQ:BAF:LRR 0/0:0.498627:0.0104211568832:0.0222474 +4 169204597 newrs150794038 G A . PASS . GT:GQ:BAF:LRR 0/0:0.500974:0.0:0.252788 +4 170190228 newrs150585496 C A . PASS . GT:GQ:BAF:LRR 0/0:0.514203:0.0:0.0413681 +4 178354368 newrs149870867 C T . PASS . GT:GQ:BAF:LRR 0/0:0.511559:0.0:0.124945 +4 184585162 newrs150331292 C T . PASS . GT:GQ:BAF:LRR 0/0:0.45756:0.0:0.0838093 +4 184605164 newrs150383310 G A . PASS . GT:GQ:BAF:LRR 0/0:0.500987:0.0125321149826:0.0583266 +4 186329171 newrs150505755 G T . PASS . GT:GQ:BAF:LRR 0/0:0.466408:0.000649333000183:0.103331 +5 6602573 newrs149980835 C T . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.117721 +5 7867002 newrs148214151 G A . PASS . GT:GQ:BAF:LRR 0/0:0.518452:0.0:-0.193469 +5 7886799 newrs147960130 C T . PASS . GT:GQ:BAF:LRR 0/0:0.517655:0.0116109848022:0.00421104 +5 7895862 newrs147277149 C T . PASS . GT:GQ:BAF:LRR 0/0:0.496997:0.0:-0.0219137 +5 32268852 newrs150354971 G A . PASS . GT:GQ:BAF:LRR 0/0:0.489312:0.0211846828461:-0.223896 +5 34005987 newrs149566702 G A . PASS . GT:GQ:BAF:LRR 0/0:0.516492:0.0:-0.31821 +5 34937509 newrs150576702 C T . PASS . GT:GQ:BAF:LRR 0/0:0.43061:0.0:-0.357641 +5 36037996 newrs147315371 G A . PASS . GT:GQ:BAF:LRR 0/0:0.495417:0.0:0.0969049 +5 37121858 newrs150242262 G A . PASS . GT:GQ:BAF:LRR 0/0:0.471498:0.0:-0.033777 +5 37153889 newrs150273774 C A . PASS . GT:GQ:BAF:LRR 0/0:0.476623:0.00462007522583:-0.918966 +5 41381928 newrs147819890 C T . PASS . GT:GQ:BAF:LRR 0/0:0.506588:0.0:-0.0765792 +5 54456071 newrs148475851 G A . PASS . GT:GQ:BAF:LRR 0/0:0.511547:0.0:-0.134849 +5 68616173 newrs148555744 C T . PASS . GT:GQ:BAF:LRR 0/0:0.422314:0.0:0.113655 +5 72419522 newrs149489778 C T . PASS . GT:GQ:BAF:LRR 0/0:0.484685:0.0:0.0821432 +5 72850781 newrs150789725 G A . PASS . GT:GQ:BAF:LRR 0/0:0.503986:0.0:-0.0377243 +5 89943581 newrs148097083 G A . PASS . GT:GQ:BAF:LRR 0/0:0.514086:0.0:0.00888062 +5 95152324 newrs146662850 G A . PASS . GT:GQ:BAF:LRR 0/0:0.262222:0.0215516090393:0.0030124 +5 95761545 newrs146545244 C T . PASS . GT:GQ:BAF:LRR 0/0:0.479755:0.0151836872101:-0.0912683 +5 96079442 newrs147728486 C T . PASS . GT:GQ:BAF:LRR 0/0:0.390289:0.0:0.0202716 +5 96130793 newrs150415434 C A . PASS . GT:GQ:BAF:LRR 0/0:0.416686:0.00451338291168:0.00768689 +5 96512820 newrs150431916 C T . PASS . GT:GQ:BAF:LRR 0/0:0.499582:0.0240887403488:-0.285518 +5 109181564 newrs147671879 A G . PASS . GT:GQ:BAF:LRR 0/0:0.500193:0.0:-0.400719 +5 121767699 newrs148152880 C T . PASS . GT:GQ:BAF:LRR 0/0:0.805341:0.0:-0.137478 +5 125894990 newrs148052962 G A . PASS . GT:GQ:BAF:LRR 0/0:0.4052:0.00488156080246:-0.0586135 +5 127595252 newrs150258538 G T . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.0:0.05085 +5 131822691 newrs146963938 G A . PASS . GT:GQ:BAF:LRR 0/0:0.431821:0.0:-0.000399141 +5 132088556 newrs148377101 A G . PASS . GT:GQ:BAF:LRR 0/0:0.401343:0.000387462:-0.157524 +5 134305783 newrs149256453 G A . PASS . GT:GQ:BAF:LRR 0/0:0.517732:0.0:0.000592531 +5 137520544 newrs150082210 C T . PASS . GT:GQ:BAF:LRR 0/0:0.493274:0.0:-0.321731 +5 138386706 newrs149242794 G A . PASS . GT:GQ:BAF:LRR 0/0:0.401577:0.0:-0.0261099 +5 140603105 newrs147283704 C T . PASS . GT:GQ:BAF:LRR 0/0:0.51489:0.0:-0.283637 +5 140625576 newrs146617445 G T . PASS . GT:GQ:BAF:LRR 0/0:0.519132:0.0:0.0242016 +5 140699110 newrs147266787 G A . PASS . GT:GQ:BAF:LRR 0/0:0.429249:0.0:-0.0930003 +5 145483756 newrs147348129 C T . PASS . GT:GQ:BAF:LRR 0/0:0.499212:0.0:-0.104196 +5 149310680 newrs146591309 G A . PASS . GT:GQ:BAF:LRR 0/0:0.4986:0.0:-0.165184 +5 151304053 newrs146895517 A G . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.0:0.104102 +5 159821492 newrs149228364 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.167868 +5 162902464 newrs146791423 G T . PASS . GT:GQ:BAF:LRR 0/0:0.518293:0.0:0.23307 +5 171849419 newrs147770326 C T . PASS . GT:GQ:BAF:LRR 0/0:0.41841:0.00467300415039:0.0520086 +5 177576841 newrs149168003 T C . PASS . GT:GQ:BAF:LRR 0/0:0.376958:0.0:0.146319 +5 178045649 newrs149761770 G A . PASS . GT:GQ:BAF:LRR 0/0:0.468639:0.0:0.0817839 +5 179674439 newrs147368192 G A . PASS . GT:GQ:BAF:LRR 0/0:0.485271:0.0:-0.361344 +6 2838116 newrs150484232 C T . PASS . GT:GQ:BAF:LRR 0/0:0.498202:0.0:0.112473 +6 2838782 newrs149196414 C T . PASS . GT:GQ:BAF:LRR 0/0:0.475714:0.0129316449165:-0.0603951 +6 4126368 newrs146626003 C T . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.0346471 +6 6224918 newrs150769138 C A . PASS . GT:GQ:BAF:LRR 0/0:0.480839:0.0:0.127136 +6 6266983 newrs150249786 G A . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.00547230243683:0.0509329 +6 7575014 newrs150339369 C T . PASS . GT:GQ:BAF:LRR 0/0:0.506698:0.00043797492981:0.100094 +6 7605637 newrs149913039 C T . PASS . GT:GQ:BAF:LRR 0/0:0.451234:0.0:0.0831667 +6 14135393 newrs149141188 C T . PASS . GT:GQ:BAF:LRR 0/0:0.410023:0.00212788581848:0.149121 +6 16274728 newrs149938350 G A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:-0.0883985 +6 17649394 newrs146704071 C T . PASS . GT:GQ:BAF:LRR 0/0:0.49999:0.0:-0.0675051 +6 24146082 newrs146546083 C T . PASS . GT:GQ:BAF:LRR 0/0:0.412921:0.0:0.225241 +6 28200588 newrs147858031 C T . PASS . GT:GQ:BAF:LRR 0/0:0.486809:0.0:-0.124464 +6 28966574 newrs149098069 G A . PASS . GT:GQ:BAF:LRR 0/0:0.517427:0.0:0.0762433 +6 29323270 newrs148190376 G A . PASS . GT:GQ:BAF:LRR 0/0:0.444712:0.000287234783173:-0.0283781 +6 29638498 newrs150133803 C T . PASS . GT:GQ:BAF:LRR 0/0:0.514336:0.0:0.12948 +6 31711970 newrs147515280 C T . PASS . GT:GQ:BAF:LRR 0/0:0.46247:0.0:-0.756938 +6 33237519 newrs146797459 A G . PASS . GT:GQ:BAF:LRR 0/0:0.41844:0.0562754:-0.680694 +6 35923138 newrs148376118 G A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.0301241 +6 36044385 newrs150550578 C T . PASS . GT:GQ:BAF:LRR 0/0:0.402972:0.0:-0.0427638 +6 38654668 newrs150725457 G A . PASS . GT:GQ:BAF:LRR 0/0:0.511761:0.0:-0.157295 +6 39325151 newrs147669724 C T . PASS . GT:GQ:BAF:LRR 0/0:0.515761:0.0:-0.330397 +6 39512364 newrs149018745 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.174162 +6 42689619 newrs146703538 T C . PASS . GT:GQ:BAF:LRR 0/0:0.73852:0.0:0.221439 +6 44217441 newrs148434564 G A . PASS . GT:GQ:BAF:LRR 1/1:0.189612:0.929015055299:0.0806835 +6 44376337 newrs148664123 C T . PASS . GT:GQ:BAF:LRR 0/0:0.473817:0.0:0.207414 +6 49604373 newrs148576118 A C . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:0.091221 +6 49665572 newrs147611117 C T . PASS . GT:GQ:BAF:LRR 0/0:0.467283:0.00373607873917:-0.00609951 +6 49986840 newrs150306060 T C . PASS . GT:GQ:BAF:LRR 0/0:0.361595:0.0:-0.366178 +6 51524480 newrs148617572 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.0556861 +6 51612695 newrs146649803 C A . PASS . GT:GQ:BAF:LRR 0/0:0.430716:0.0624964237213:-0.62797 +6 51944754 newrs149841071 C T . PASS . GT:GQ:BAF:LRR 0/0:0.513663:0.0:0.0043441 +6 54245326 newrs147405762 G A . PASS . GT:GQ:BAF:LRR 0/0:0.348161:0.0:0.02333 +6 56031702 newrs149344559 A C . PASS . GT:GQ:BAF:LRR 0/0:0.499112:0.0189819:-0.921558 +6 70745831 newrs148417796 T G . PASS . GT:GQ:BAF:LRR 0/0:0.499281:0.0:-0.143673 +6 70886456 newrs149084573 G A . PASS . GT:GQ:BAF:LRR 0/0:0.518369:0.0:-0.187747 +6 71235565 newrs147626858 A G . PASS . GT:GQ:BAF:LRR 0/0:0.446692:0.0:0.246924 +6 79735234 newrs150666163 A C . PASS . GT:GQ:BAF:LRR 0/0:0.502405:0.00637529:-0.204842 +6 80878661 newrs149766077 C T . PASS . GT:GQ:BAF:LRR 0/0:0.511074:0.00449514389038:0.0435437 +6 88128008 newrs150688579 C A . PASS . GT:GQ:BAF:LRR 0/0:0.48702:0.00954270362854:0.0114397 +6 88854927 newrs148575019 C T . PASS . GT:GQ:BAF:LRR 0/0:0.405282:0.0183826088905:0.0457113 +6 97726724 newrs149389562 C T . PASS . GT:GQ:BAF:LRR 0/0:0.511947:0.0:-1.0419 +6 101246588 newrs149330987 C T . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.22692 +6 110083316 newrs149991846 C T . PASS . GT:GQ:BAF:LRR 0/0:0.514177:0.0:0.0147441 +6 116381238 newrs148677068 C T . PASS . GT:GQ:BAF:LRR 0/0:0.444153:0.0:0.0649031 +6 117130477 newrs148056762 C T . PASS . GT:GQ:BAF:LRR 0/0:0.51585:0.00232928991318:0.196313 +6 117714485 newrs150002762 C T . PASS . GT:GQ:BAF:LRR 0/0:0.460902:0.0:0.153582 +6 126342411 newrs147290904 G A . PASS . GT:GQ:BAF:LRR 0/0:0.488048:0.0:-0.0512607 +6 129591829 newrs149896793 G T . PASS . GT:GQ:BAF:LRR 0/0:0.879453:0.0:-0.0549465 +6 129823916 newrs149210847 G A . PASS . GT:GQ:BAF:LRR 0/0:0.443605:0.0:-0.0520813 +6 131903787 newrs146625637 G A . PASS . GT:GQ:BAF:LRR 0/0:0.477381:0.0:-0.46777 +6 131917198 newrs150404447 G A . PASS . GT:GQ:BAF:LRR ./.:0.147684:0.0924681425095:-0.537138 +6 131971260 newrs148423655 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.305997 +6 132860014 newrs148058947 C T . PASS . GT:GQ:BAF:LRR 0/0:0.765983:2.89082527161e-05:0.120775 +6 133072307 newrs148308586 G A . PASS . GT:GQ:BAF:LRR 0/0:0.393705:0.0:0.119613 +6 133091438 newrs147790535 G A . PASS . GT:GQ:BAF:LRR 0/0:0.499844:0.00934100151062:-0.197474 +6 135644371 newrs148000791 T C . PASS . GT:GQ:BAF:LRR 0/0:0.769926:0.00590789:-0.0474465 +6 144167206 newrs147204809 C T . PASS . GT:GQ:BAF:LRR 0/0:0.361595:0.000106871128082:0.0918177 +6 150067220 newrs149249345 C T . PASS . GT:GQ:BAF:LRR 0/0:0.829428:0.0163365602493:-0.467624 +6 151142369 newrs147160033 G A . PASS . GT:GQ:BAF:LRR 0/0:0.470049:0.0:-0.0240805 +6 151198963 newrs148145283 G A . PASS . GT:GQ:BAF:LRR 0/0:0.495932:0.0016867518425:0.18917 +6 159086426 newrs149940898 G A . PASS . GT:GQ:BAF:LRR 0/0:0.496902:0.0:-0.173953 +6 160206506 newrs147224137 C A . PASS . GT:GQ:BAF:LRR 0/0:0.517088:0.0:0.142711 +6 166576109 newrs146708556 C T . PASS . GT:GQ:BAF:LRR 0/0:0.472919:0.0:0.069307 +7 6094176 newrs148495208 C T . PASS . GT:GQ:BAF:LRR 0/0:0.494974:0.0:0.218663 +7 7398347 newrs148652610 G A . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:-0.0484772 +7 7420436 newrs146560754 C A . PASS . GT:GQ:BAF:LRR 0/0:0.498756:0.0:-0.837225 +7 16901072 newrs147702108 C T . PASS . GT:GQ:BAF:LRR 0/0:0.503938:0.0:0.0794229 +7 20687233 newrs150279505 C T . PASS . GT:GQ:BAF:LRR 0/0:0.626366:0.0:0.052956 +7 20795056 newrs146527949 C T . PASS . GT:GQ:BAF:LRR 0/0:0.823854:0.0:0.171989 +7 21760479 newrs149364992 G A . PASS . GT:GQ:BAF:LRR 0/0:0.512487:0.0:-0.0419911 +7 31015394 newrs146944568 G T . PASS . GT:GQ:BAF:LRR 0/0:0.498177:0.0:-0.221978 +7 31682773 newrs147656859 C T . PASS . GT:GQ:BAF:LRR 0/0:0.376958:0.00934475660324:0.0268844 +7 37953975 newrs146871972 C T . PASS . GT:GQ:BAF:LRR 0/0:0.438034:0.0:-0.136432 +7 48068485 newrs146974310 G T . PASS . GT:GQ:BAF:LRR 0/0:0.504407:0.0:-0.946155 +7 66458309 newrs148500031 T G . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.0:0.0321762 +7 72745738 newrs147213094 C T . PASS . GT:GQ:BAF:LRR 0/0:0.876565:0.0:-0.0771317 +7 78150747 newrs146782279 C T . PASS . GT:GQ:BAF:LRR 0/0:0.498423:0.0:0.0804179 +7 83606448 newrs149706425 C T . PASS . GT:GQ:BAF:LRR 0/0:0.496814:0.0:0.146361 +7 87053223 newrs147134978 G A . PASS . GT:GQ:BAF:LRR 0/0:0.424438:0.00156581401825:0.146698 +7 89856411 newrs148055758 C T . PASS . GT:GQ:BAF:LRR ./.:0.034817:0.109675884247:0.144389 +7 92147282 newrs149806989 G A . PASS . GT:GQ:BAF:LRR 0/0:0.470185:0.0:0.0028629 +7 92734725 newrs147146654 G T . PASS . GT:GQ:BAF:LRR 0/0:0.461277:0.0:0.065138 +7 93125288 newrs148624177 T C . PASS . GT:GQ:BAF:LRR 0/0:0.862597:0.00648627:-0.271906 +7 94947635 newrs149100710 C T . PASS . GT:GQ:BAF:LRR 0/0:0.419162:0.0:0.164907 +7 98951744 newrs150004356 A G . PASS . GT:GQ:BAF:LRR 0/0:0.85023:0.0431999:-0.057032 +7 99021454 newrs147029104 C A . PASS . GT:GQ:BAF:LRR 0/0:0.376958:0.0:0.0332874 +7 99056770 newrs146584377 T G . PASS . GT:GQ:BAF:LRR 0/0:0.310014:0.0151878:0.107117 +7 99447238 newrs146587177 C T . PASS . GT:GQ:BAF:LRR 0/0:0.479159:0.0050385594368:-0.0913506 +7 99461224 newrs149091175 C T . PASS . GT:GQ:BAF:LRR 0/0:0.412935:0.0155234336853:0.008036 +7 100682921 newrs148241944 C T . PASS . GT:GQ:BAF:LRR 0/0:0.49213:0.0:-0.00512057 +7 100701287 newrs148704443 C T . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.132494 +7 102572363 newrs149803390 G A . PASS . GT:GQ:BAF:LRR 0/0:0.466583:0.0368211269379:-0.0119469 +7 103194107 newrs149473868 G A . PASS . GT:GQ:BAF:LRR 0/0:0.497895:0.0:-0.288528 +7 107330644 newrs147952620 C T . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.0744032 +7 107389484 newrs147566750 G A . PASS . GT:GQ:BAF:LRR 0/0:0.500344:0.0:0.0364388 +7 107571875 newrs150279683 G A . PASS . GT:GQ:BAF:LRR 0/0:0.510223:0.0:-0.191995 +7 107720186 newrs149878640 C A . PASS . GT:GQ:BAF:LRR 0/0:0.516101:0.0:-0.0543236 +7 117175437 newrs147432698 G A . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:0.0265408 +7 117282649 newrs146795445 T C . PASS . GT:GQ:BAF:LRR 0/0:0.495513:0.0:0.0273504 +7 117304901 newrs146947665 C A . PASS . GT:GQ:BAF:LRR 0/0:0.37779:0.0:-0.209502 +7 120972020 newrs148077060 T C . PASS . GT:GQ:BAF:LRR 0/0:0.472943:0.0:0.224081 +7 122338300 newrs150520039 G A . PASS . GT:GQ:BAF:LRR 0/0:0.411296:0.0:-0.202642 +7 128049368 newrs147481910 G A . PASS . GT:GQ:BAF:LRR 0/0:0.494525:0.00300014019012:-0.3465 +7 129102806 newrs150375291 G A . PASS . GT:GQ:BAF:LRR 0/0:0.39855:0.0:0.0763563 +7 130140359 newrs150557584 T C . PASS . GT:GQ:BAF:LRR 0/0:0.371084:0.0:0.0972567 +7 130297018 newrs149067956 A C . PASS . GT:GQ:BAF:LRR 0/0:0.402212:0.0:-0.0416476 +7 134346603 newrs149329328 G A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:-0.058507 +7 134743986 newrs148387846 G A . PASS . GT:GQ:BAF:LRR 0/0:0.517484:0.0:0.16241 +7 138453918 newrs146911574 G A . PASS . GT:GQ:BAF:LRR 0/0:0.517328:0.0:0.00369581 +7 140037084 newrs150070842 C A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.000719308853149:0.0970307 +7 141957488 newrs149822174 C T . PASS . GT:GQ:BAF:LRR 0/0:0.449554:0.00251418352127:0.0227259 +7 142723442 newrs147956738 G A . PASS . GT:GQ:BAF:LRR 0/0:0.416461:0.0:0.0851405 +7 151704910 newrs148226163 A G . PASS . GT:GQ:BAF:LRR 0/0:0.418337:0.0:0.123419 +7 156516874 newrs148655712 T C . PASS . GT:GQ:BAF:LRR 0/0:0.508644:0.0:0.0939681 +8 6728244 newrs148577927 G A . PASS . GT:GQ:BAF:LRR 0/0:0.48212:0.0:-0.062812 +8 17412208 newrs149207619 G A . PASS . GT:GQ:BAF:LRR 0/0:0.385962:0.0171897411346:0.00994784 +8 19819645 newrs149089920 G A . PASS . GT:GQ:BAF:LRR 0/0:0.50382:0.0:0.110698 +8 29923547 newrs149135189 A C . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.0941432 +8 29924293 newrs150321308 C T . PASS . GT:GQ:BAF:LRR 0/0:0.431675:0.0:0.150147 +8 55013468 newrs146719663 C T . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:0.0428714 +8 59720335 newrs148474393 G A . PASS . GT:GQ:BAF:LRR 0/0:0.491209:0.0:0.00992137 +8 62559438 newrs148798777 C T . PASS . GT:GQ:BAF:LRR 0/0:0.390176:0.0360451936722:-0.316261 +8 92378808 newrs149167044 G T . PASS . GT:GQ:BAF:LRR 0/0:0.487412:0.0348261594772:-1.02679 +8 94809573 newrs150332116 C T . PASS . GT:GQ:BAF:LRR 0/0:0.47997:0.0:-0.148844 +8 95780690 newrs147961118 C T . PASS . GT:GQ:BAF:LRR 0/0:0.512505:0.0:-0.740395 +8 98817694 newrs146674780 T G . PASS . GT:GQ:BAF:LRR 0/0:0.477981:0.0:-0.183789 +8 99153059 newrs149102421 C T . PASS . GT:GQ:BAF:LRR 0/0:0.516508:0.0:-0.0896263 +8 105360974 newrs149253106 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.0334924 +8 113243773 newrs148762244 C T . PASS . GT:GQ:BAF:LRR 0/0:0.496741:0.0:0.0121333 +8 113529404 newrs149308903 G A . PASS . GT:GQ:BAF:LRR 0/0:0.406537:0.0889647006989:-0.634537 +8 120079545 newrs149010496 C T . PASS . GT:GQ:BAF:LRR 0/0:0.5093:0.0:-0.0297208 +8 121528432 newrs146791881 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.00410368 +8 124153064 newrs147736638 C T . PASS . GT:GQ:BAF:LRR 0/0:0.50028:0.00956904888153:-0.0463144 +8 125988753 newrs146924154 G A . PASS . GT:GQ:BAF:LRR 0/0:0.511391:0.00474852323532:-0.186399 +8 125989242 newrs147804097 T G . PASS . GT:GQ:BAF:LRR 0/0:0.528154:0.0:0.0763266 +8 126091058 newrs150749307 A C . PASS . GT:GQ:BAF:LRR 0/0:0.409735:0.0:0.0371055 +8 131793034 newrs150698439 G A . PASS . GT:GQ:BAF:LRR 0/0:0.40745:0.00228369235992:-0.145221 +8 133045281 newrs150715638 C T . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.00408619 +8 139647253 newrs147655243 T C . PASS . GT:GQ:BAF:LRR 0/0:0.496736:0.0:-0.095211 +8 141828445 newrs149643582 C T . PASS . GT:GQ:BAF:LRR 0/0:0.429057:0.0:0.0567128 +8 143922641 newrs150041552 C T . PASS . GT:GQ:BAF:LRR 0/0:0.379684:0.0:0.102652 +8 145541643 newrs149913927 G A . PASS . GT:GQ:BAF:LRR 0/0:0.501834:0.0:0.341797 +9 730250 newrs149121553 T G . PASS . GT:GQ:BAF:LRR 0/0:0.443413:0.0:0.0804472 +9 6620265 newrs147066809 C T . PASS . GT:GQ:BAF:LRR 0/0:0.498822:0.000689148902893:-0.0930856 +9 12695801 newrs147425437 C T . PASS . GT:GQ:BAF:LRR 0/0:0.49518:0.0:0.00874371 +9 14313479 newrs149244411 A G . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:0.172245 +9 15189604 newrs150307895 G A . PASS . GT:GQ:BAF:LRR 0/0:0.460868:0.0:-0.0418732 +9 15777824 newrs150773145 G A . PASS . GT:GQ:BAF:LRR 0/0:0.507443:0.0:-0.245318 +9 23704916 newrs149957439 C T . PASS . GT:GQ:BAF:LRR 0/0:0.409735:0.0:0.127377 +9 32418196 newrs150497498 G T . PASS . GT:GQ:BAF:LRR 0/0:0.391281:0.00188255310059:0.0385714 +9 35105838 newrs150293710 T C . PASS . GT:GQ:BAF:LRR 0/0:0.374745:0.015341:-0.344273 +9 36229085 newrs150132839 G A . PASS . GT:GQ:BAF:LRR 0/0:0.463932:0.0:0.0214163 +9 36246023 newrs150714953 C T . PASS . GT:GQ:BAF:LRR 0/0:0.452542:0.0:-0.05807 +9 36599448 newrs149686898 G T . PASS . GT:GQ:BAF:LRR 0/0:0.498642:0.00392311811447:-0.0183786 +9 71842791 newrs146543810 T C . PASS . GT:GQ:BAF:LRR 0/0:0.483202:0.0194993:-0.407073 +9 72090963 newrs146989913 C T . PASS . GT:GQ:BAF:LRR 0/0:0.39031:0.00765013694763:0.110792 +9 80049440 newrs148017027 T C . PASS . GT:GQ:BAF:LRR 0/0:0.37316:0.0:-0.778066 +9 88694215 newrs150427559 C A . PASS . GT:GQ:BAF:LRR 0/0:0.837281:0.0:-0.505544 +9 90584745 newrs150288403 C T . PASS . GT:GQ:BAF:LRR 0/0:0.438569:0.0:-0.173952 +9 95236930 newrs148382623 G A . PASS . GT:GQ:BAF:LRR 0/0:0.517606:0.0:-0.0564555 +9 99150527 newrs149972653 G A . PASS . GT:GQ:BAF:LRR 0/0:0.507227:0.0:-0.194281 +9 99521480 newrs148296433 G T . PASS . GT:GQ:BAF:LRR 0/0:0.320932:0.0:-0.0681799 +9 101611350 newrs146530383 G A . PASS . GT:GQ:BAF:LRR 0/0:0.516196:0.0:0.0148138 +9 103027123 newrs149055711 G A . PASS . GT:GQ:BAF:LRR 0/0:0.491606:0.0:-0.704742 +9 103035281 newrs148239569 C A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.000614404678345:0.011245 +9 104153053 newrs150313404 G A . PASS . GT:GQ:BAF:LRR 0/0:0.310014:0.0:0.275689 +9 114090454 newrs147330382 G T . PASS . GT:GQ:BAF:LRR 0/0:0.499408:0.0:-0.00693784 +9 115811718 newrs149489774 C T . PASS . GT:GQ:BAF:LRR 0/0:0.496922:0.0143982172012:-0.0371306 +9 116082637 newrs148709910 C T . PASS . GT:GQ:BAF:LRR 0/0:0.445186:0.0:0.111948 +9 117066858 newrs148603511 C T . PASS . GT:GQ:BAF:LRR 0/0:0.898204:0.0:-0.0691764 +9 123779921 newrs149506797 C T . PASS . GT:GQ:BAF:LRR 0/0:0.479659:0.0:0.0266884 +9 125377927 newrs147488616 G A . PASS . GT:GQ:BAF:LRR 0/0:0.489495:0.0:-0.0757379 +9 128118071 newrs149182108 C T . PASS . GT:GQ:BAF:LRR 0/0:0.446959:0.0:-0.208093 +9 131495705 newrs148330265 C A . PASS . GT:GQ:BAF:LRR 0/0:0.437462:0.000301659107208:0.0410152 +9 131720291 newrs147379666 A C . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.085527 +9 133578458 newrs149299789 C T . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.00654429197311:0.0245837 +9 133993305 newrs146631291 T G . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.0629581 +9 135153507 newrs148041889 T C . PASS . GT:GQ:BAF:LRR 0/0:0.49797:0.0:0.0785968 +9 136219551 newrs147816470 G A . PASS . GT:GQ:BAF:LRR 0/0:0.474548:0.00285243988037:0.0567933 +10 7774310 newrs146878856 C T . PASS . GT:GQ:BAF:LRR 0/0:0.412484:0.0:-0.047972 +10 11908528 newrs148477384 A C . PASS . GT:GQ:BAF:LRR 0/0:0.399871:0.0:0.0159494 +10 13639535 newrs150642801 G A . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:0.0228095 +10 17113425 newrs149242963 C A . PASS . GT:GQ:BAF:LRR 0/0:0.514945:0.0:-0.0432116 +10 21120157 newrs149647815 G A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.0329142 +10 24880816 newrs148522047 G A . PASS . GT:GQ:BAF:LRR 0/0:0.497071:0.0:0.141646 +10 27508651 newrs150476576 C T . PASS . GT:GQ:BAF:LRR 0/0:0.529569:0.0:-0.0436874 +10 38343680 newrs148335528 G T . PASS . GT:GQ:BAF:LRR 0/0:0.467283:0.0:0.0467212 +10 43615577 newrs146838520 C T . PASS . GT:GQ:BAF:LRR 0/0:0.490596:0.0:0.0395851 +10 50916603 newrs148244498 G A . PASS . GT:GQ:BAF:LRR 0/0:0.517626:0.0:-0.456432 +10 63957819 newrs147070919 G A . PASS . GT:GQ:BAF:LRR 0/0:0.518923:0.0:-0.0639654 +10 64414691 newrs149781580 G A . PASS . GT:GQ:BAF:LRR 0/0:0.400712:0.00579476356506:0.0207258 +10 73082714 newrs148956476 G A . PASS . GT:GQ:BAF:LRR 0/0:0.499416:0.0:-0.4076 +10 75542124 newrs150644371 G A . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:-0.0799351 +10 79760832 newrs146957784 G A . PASS . GT:GQ:BAF:LRR 0/0:0.477549:0.0:0.0317019 +10 82185762 newrs150786234 G A . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:0.0422308 +10 85982437 newrs149695318 C A . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0100020766258:0.0359495 +10 90428514 newrs147791767 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519044:0.0:-0.168957 +10 92635313 newrs149794455 A G . PASS . GT:GQ:BAF:LRR 0/0:0.499538:0.00889996:-0.571601 +10 95262876 newrs146596670 C T . PASS . GT:GQ:BAF:LRR 0/0:0.336205:0.0:0.0788771 +10 96824564 newrs146962089 C T . PASS . GT:GQ:BAF:LRR 0/0:0.480633:0.0:0.137482 +10 98924593 newrs149092674 G T . PASS . GT:GQ:BAF:LRR 0/0:0.476294:0.0:-0.0925921 +10 100017402 newrs150271620 C T . PASS . GT:GQ:BAF:LRR 0/0:0.501296:0.0:-0.14171 +10 101460763 newrs147079897 C T . PASS . GT:GQ:BAF:LRR 0/0:0.440935:0.0:0.0516604 +10 101462431 newrs149232042 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.238669 +10 102013179 newrs150239404 G A . PASS . GT:GQ:BAF:LRR 0/0:0.476607:0.0:0.0762578 +10 105780318 newrs147985366 C T . PASS . GT:GQ:BAF:LRR 0/0:0.514751:0.0:-0.165547 +10 105832966 newrs147734242 A C . PASS . GT:GQ:BAF:LRR 0/0:0.351044:0.00517626:0.0590782 +10 106159259 newrs150734798 G A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0238655805588:-0.0082339 +10 114182199 newrs149581330 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.0646247 +10 120920436 newrs147648163 G A . PASS . GT:GQ:BAF:LRR 0/0:0.515544:0.0193114280701:-0.0458524 +10 124708272 newrs147972795 C T . PASS . GT:GQ:BAF:LRR 0/0:0.884711:0.0:-0.0281962 +10 126453960 newrs147429177 C T . PASS . GT:GQ:BAF:LRR 0/0:0.514392:0.0:0.123145 +10 127456101 newrs146637402 A G . PASS . GT:GQ:BAF:LRR 0/0:0.495607:0.0:0.03097 +10 127519995 newrs147798836 C T . PASS . GT:GQ:BAF:LRR 0/0:0.495904:0.0:0.0649443 +11 1092350 newrs146769199 G T . PASS . GT:GQ:BAF:LRR 0/0:0.464376:0.0:0.137696 +11 3845507 newrs147354096 C T . PASS . GT:GQ:BAF:LRR 0/0:0.504719:0.004449903965:-0.256221 +11 5686886 newrs150799809 C T . PASS . GT:GQ:BAF:LRR 0/0:0.511202:0.0:0.04264 +11 6129810 newrs150485733 C T . PASS . GT:GQ:BAF:LRR 0/0:0.41881:0.0:0.264216 +11 6220736 newrs149905780 C T . PASS . GT:GQ:BAF:LRR 0/0:0.517395:0.000857532024384:-0.273309 +11 6262908 newrs150327554 C T . PASS . GT:GQ:BAF:LRR 0/0:0.426473:0.0:0.121701 +11 6913227 newrs148113613 G A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.0696338 +11 7672131 newrs149262617 C T . PASS . GT:GQ:BAF:LRR 0/0:0.473034:0.0359147787094:-0.104774 +11 7949333 newrs147185885 G A . PASS . GT:GQ:BAF:LRR 0/0:0.421756:0.0:-0.0509975 +11 8120422 newrs147394931 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.112725 +11 10518408 newrs147243781 G T . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.00283265113831:-0.0167666 +11 10555597 newrs149870408 C A . PASS . GT:GQ:BAF:LRR 0/0:0.511667:0.000948667526245:-0.185732 +11 10585814 newrs149004349 C A . PASS . GT:GQ:BAF:LRR 0/0:0.510589:0.0:-0.0579392 +11 16424346 newrs147886976 C T . PASS . GT:GQ:BAF:LRR 0/0:0.509721:0.0:0.0419625 +11 17542960 newrs147956944 T G . PASS . GT:GQ:BAF:LRR 0/0:0.404434:0.0:-0.16419 +11 19077207 newrs150168108 C T . PASS . GT:GQ:BAF:LRR 0/0:0.495872:0.0:0.139944 +11 19246240 newrs150255844 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.507128 +11 30937137 newrs150388476 G A . PASS . GT:GQ:BAF:LRR 0/0:0.49798:0.0:0.0827253 +11 34165021 newrs148378865 G A . PASS . GT:GQ:BAF:LRR 0/0:0.506558:0.0:0.100185 +11 34979130 newrs148117169 G A . PASS . GT:GQ:BAF:LRR 0/0:0.443788:0.0:0.13915 +11 47298298 newrs147179561 C T . PASS . GT:GQ:BAF:LRR 0/0:0.442723:0.00542795658112:0.00624628 +11 47690393 newrs150818119 C T . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.00559258460999:-0.00667744 +11 55339895 newrs149911886 C T . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.0:-0.0346859 +11 57148121 newrs149309930 C T . PASS . GT:GQ:BAF:LRR 0/0:0.451699:0.0:-0.0227875 +11 58491889 newrs150657394 C T . PASS . GT:GQ:BAF:LRR 0/0:0.499688:0.0:-0.11501 +11 59224880 newrs146734452 G A . PASS . GT:GQ:BAF:LRR ./.:0.0677895:0.0205971002579:-1.62045 +11 59810966 newrs149225217 G A . PASS . GT:GQ:BAF:LRR 0/0:0.511847:0.0:0.0935151 +11 60183438 newrs150784858 C T . PASS . GT:GQ:BAF:LRR 0/0:0.374745:0.0104249119759:0.0299738 +11 60268634 newrs150012278 C A . PASS . GT:GQ:BAF:LRR 0/0:0.517754:0.0:-0.235949 +11 62502922 newrs150104999 C T . PASS . GT:GQ:BAF:LRR 0/0:0.513799:0.0:-0.0566828 +11 62652683 newrs147281603 C T . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.0:0.0194589 +11 64004657 newrs147883767 A G . PASS . GT:GQ:BAF:LRR 0/0:0.39033:0.0086501:-0.292782 +11 73610190 newrs147312150 G A . PASS . GT:GQ:BAF:LRR 0/0:0.489787:0.0203649997711:-0.0325025 +11 82625793 newrs147443808 C T . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.0118647 +11 82947475 newrs150299461 C T . PASS . GT:GQ:BAF:LRR 0/0:0.511187:0.0:-0.201803 +11 85444980 newrs146718885 A G . PASS . GT:GQ:BAF:LRR 0/0:0.489319:0.0:-0.246762 +11 86108785 newrs150754388 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.108652 +11 86126234 newrs147662103 C T . PASS . GT:GQ:BAF:LRR 0/0:0.517304:0.0:-0.483553 +11 88911706 newrs147574809 G A . PASS . GT:GQ:BAF:LRR 0/0:0.516684:0.0:-0.237684 +11 88961060 newrs149912348 A G . PASS . GT:GQ:BAF:LRR 0/0:0.529569:0.0:0.0785688 +11 94134180 newrs148986490 G T . PASS . GT:GQ:BAF:LRR 0/0:0.435487:0.00298118591309:0.00131885 +11 102562717 newrs149812545 G T . PASS . GT:GQ:BAF:LRR 0/0:0.491768:0.0:0.148066 +11 102573704 newrs148894063 G A . PASS . GT:GQ:BAF:LRR 0/0:0.429207:0.0:0.0653236 +11 104916018 newrs150516068 C T . PASS . GT:GQ:BAF:LRR 0/0:0.40302:0.0:-0.168883 +11 108158399 newrs147600485 A G . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.308222 +11 108332229 newrs149955947 G A . PASS . GT:GQ:BAF:LRR 0/0:0.502425:0.0:0.119168 +11 108381145 newrs149024755 G A . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:0.121641 +11 111888614 newrs150406695 A G . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:0.0611805 +11 112104210 newrs150726932 G T . PASS . GT:GQ:BAF:LRR 0/0:0.510946:0.0:0.127193 +11 113614519 newrs150184757 C T . PASS . GT:GQ:BAF:LRR 0/0:0.864861:0.0:0.110055 +11 118531332 newrs147240748 G A . PASS . GT:GQ:BAF:LRR 0/0:0.495879:0.0:-0.0928038 +11 119042182 newrs148683955 G A . PASS . GT:GQ:BAF:LRR 0/0:0.451091:0.0:-0.208553 +11 119167745 newrs148996708 G A . PASS . GT:GQ:BAF:LRR 0/0:0.483076:0.0399552583694:-0.222996 +11 124496808 newrs149295558 C T . PASS . GT:GQ:BAF:LRR 0/0:0.499712:0.0:-0.052869 +11 124761459 newrs147387634 C T . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.0475243 +11 125766086 newrs147862544 G A . PASS . GT:GQ:BAF:LRR 0/0:0.336045:0.0091450214386:0.121075 +11 125864808 newrs149220812 G T . PASS . GT:GQ:BAF:LRR 0/0:0.511512:0.000152826309204:0.118508 +11 133715087 newrs150527694 T G . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:0.000637571 +11 134010629 newrs146878298 C T . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.0309197 +11 134121125 newrs149874205 G A . PASS . GT:GQ:BAF:LRR 0/0:0.517529:0.0:0.0266778 +12 547528 newrs149946039 T G . PASS . GT:GQ:BAF:LRR 0/0:0.526609:0.0:-0.125997 +12 6182789 newrs147924974 G T . PASS . GT:GQ:BAF:LRR 0/0:0.348259:0.0:0.121485 +12 6631204 newrs149296057 G A . PASS . GT:GQ:BAF:LRR 0/0:0.517516:0.0:0.18005 +12 7043191 newrs147637415 G A . PASS . GT:GQ:BAF:LRR 0/0:0.517448:0.0:0.220633 +12 8212133 newrs149088151 G A . PASS . GT:GQ:BAF:LRR 0/0:0.434579:0.0:0.0347664 +12 9318694 newrs150067154 G A . PASS . GT:GQ:BAF:LRR 0/0:0.511852:0.0:0.0547247 +12 9353641 newrs147359935 G A . PASS . GT:GQ:BAF:LRR 0/0:0.494992:0.00515085458755:-0.42624 +12 10167887 newrs148805742 G A . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:0.0744616 +12 11138813 newrs146930737 G T . PASS . GT:GQ:BAF:LRR 0/0:0.444634:0.0:-0.0895737 +12 11175056 newrs146593308 G A . PASS . GT:GQ:BAF:LRR 0/0:0.517591:0.0:0.132098 +12 11507474 newrs149040356 C A . PASS . GT:GQ:BAF:LRR 0/0:0.495418:0.0:-0.514673 +12 13220190 newrs148941252 C T . PASS . GT:GQ:BAF:LRR 0/0:0.492975:0.0:-0.221685 +12 15679198 newrs150178443 T C . PASS . GT:GQ:BAF:LRR 0/0:0.491291:0.0:-0.0348158 +12 21799831 newrs149479698 A G . PASS . GT:GQ:BAF:LRR 0/0:0.499838:0.0:-0.391543 +12 25679747 newrs150558545 G A . PASS . GT:GQ:BAF:LRR 0/0:0.498379:0.0:0.133149 +12 29460778 newrs148185891 C A . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:-0.0190527 +12 30790063 newrs148376849 G A . PASS . GT:GQ:BAF:LRR 0/0:0.415368:0.0:-0.0387285 +12 30864505 newrs150085536 G A . PASS . GT:GQ:BAF:LRR 0/0:0.403649:0.0:-0.186096 +12 32138688 newrs147453939 T G . PASS . GT:GQ:BAF:LRR 0/0:0.436548:0.0:-0.189563 +12 40001518 newrs147085772 T G . PASS . GT:GQ:BAF:LRR 0/0:0.500162:0.0:-0.219847 +12 40653379 newrs150368439 C T . PASS . GT:GQ:BAF:LRR 0/0:0.498608:0.0:-0.114147 +12 41421776 newrs148453314 A G . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:0.0264907 +12 48110672 newrs150299683 C T . PASS . GT:GQ:BAF:LRR 0/0:0.49919:0.0:0.0169383 +12 49255792 newrs147876425 C T . PASS . GT:GQ:BAF:LRR 0/0:0.897003:0.0:-0.295595 +12 49460259 newrs148047837 C T . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.0:0.121282 +12 51393026 newrs150400273 T C . PASS . GT:GQ:BAF:LRR 0/0:0.458406:0.00810786:-1.05378 +12 52912732 newrs147185753 G A . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.00681835412979:-0.177377 +12 56522494 newrs147784540 G T . PASS . GT:GQ:BAF:LRR 0/0:0.412205:0.0:-0.193535 +12 56817237 newrs149262573 G A . PASS . GT:GQ:BAF:LRR 0/0:0.376958:0.00743329524994:-0.166376 +12 56868326 newrs146654208 A G . PASS . GT:GQ:BAF:LRR 0/0:0.500032:0.0:0.0307203 +12 56975233 newrs146998541 C T . PASS . GT:GQ:BAF:LRR 0/0:0.351044:0.0:-0.0827936 +12 57431332 newrs149628462 A G . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:-0.0208024 +12 57454555 newrs149540426 C T . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.226693 +12 71533491 newrs146656002 C A . PASS . GT:GQ:BAF:LRR 0/0:0.486986:0.00406295061111:-0.0547003 +12 85255518 newrs146589974 G A . PASS . GT:GQ:BAF:LRR 0/0:0.493611:0.0:-0.352324 +12 85515611 newrs148400374 C T . PASS . GT:GQ:BAF:LRR 0/0:0.509903:0.0:0.121781 +12 89814944 newrs148916260 G A . PASS . GT:GQ:BAF:LRR 0/0:0.511852:0.0:-0.49853 +12 93139253 newrs149205825 G A . PASS . GT:GQ:BAF:LRR 0/0:0.418933:0.0:-0.0995775 +12 96386479 newrs149004222 G A . PASS . GT:GQ:BAF:LRR 0/0:0.493798:0.0:-0.0689596 +12 101577912 newrs149078919 C T . PASS . GT:GQ:BAF:LRR 0/0:0.515374:0.0:-0.0211334 +12 102131005 newrs149836328 G A . PASS . GT:GQ:BAF:LRR 0/0:0.499902:0.0:-0.300278 +12 102437878 newrs147510623 C T . PASS . GT:GQ:BAF:LRR 0/0:0.50465:0.0:0.226673 +12 103288566 newrs148393887 T C . PASS . GT:GQ:BAF:LRR 0/0:0.516955:0.0:-0.215266 +12 104031811 newrs149696858 C T . PASS . GT:GQ:BAF:LRR 0/0:0.396067:0.0146797895432:-0.0488444 +12 104378575 newrs149399146 C T . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.0:0.0222286 +12 106804655 newrs148879912 C T . PASS . GT:GQ:BAF:LRR 0/0:0.510047:0.0:-0.36265 +12 112940006 newrs148176616 C T . PASS . GT:GQ:BAF:LRR 0/0:0.204639:0.0:0.103787 +12 113645335 newrs147913046 G A . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:-0.0160547 +12 114804165 newrs147405081 C T . PASS . GT:GQ:BAF:LRR 0/0:0.517404:0.0:-0.0578861 +12 121008995 newrs150629669 C A . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:0.0051172 +12 121471459 newrs148845781 C A . PASS . GT:GQ:BAF:LRR 0/0:0.431302:0.0:0.107072 +12 121613282 newrs149116962 G A . PASS . GT:GQ:BAF:LRR 0/0:0.376179:0.0:0.0550921 +12 121687764 newrs147402468 T C . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.0:0.135268 +12 124097800 newrs149103406 G T . PASS . GT:GQ:BAF:LRR 0/0:0.515712:0.0:-0.000184893 +12 124114714 newrs148513104 A C . PASS . GT:GQ:BAF:LRR 0/0:0.334046:0.0115446:-0.706299 +12 124210832 newrs147005791 G A . PASS . GT:GQ:BAF:LRR 0/0:0.476306:0.00199675559998:0.133518 +12 133438222 newrs148932455 T C . PASS . GT:GQ:BAF:LRR 0/0:0.371867:0.00143908:0.123477 +13 19752385 newrs148979711 C T . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:0.113743 +13 25828033 newrs150032485 C T . PASS . GT:GQ:BAF:LRR 0/0:0.519034:0.00173681974411:0.0327747 +13 36748613 newrs148826039 C T . PASS . GT:GQ:BAF:LRR 0/0:0.403126:0.0:0.114596 +13 37569125 newrs148564105 C A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.00277745723724:-0.0530646 +13 38171321 newrs149175978 G A . PASS . GT:GQ:BAF:LRR 0/0:0.871759:0.0:0.0379355 +13 43500527 newrs149216994 G A . PASS . GT:GQ:BAF:LRR 0/0:0.499868:0.0:-0.0824176 +13 43896520 newrs147465511 C T . PASS . GT:GQ:BAF:LRR 0/0:0.421506:0.0132063031197:-0.225517 +13 45148546 newrs146993055 G A . PASS . GT:GQ:BAF:LRR 0/0:0.421133:0.0:0.0676405 +13 50275987 newrs147153406 G T . PASS . GT:GQ:BAF:LRR 0/0:0.499631:0.0:0.0184289 +13 94958377 newrs149343030 G A . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:0.11637 +13 95838955 newrs149813736 C T . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:-0.251838 +13 103525640 newrs147955525 A G . PASS . GT:GQ:BAF:LRR 0/0:0.519483:0.0:-0.290787 +13 113053487 newrs146598083 G A . PASS . GT:GQ:BAF:LRR 0/0:0.500165:0.0:-0.000879787 +13 113851339 newrs147592475 G T . PASS . GT:GQ:BAF:LRR 0/0:0.421849:0.0:0.222139 +13 114154348 newrs147239381 C T . PASS . GT:GQ:BAF:LRR 0/0:0.501994:0.0:0.0145494 +14 20848453 newrs150831074 C T . PASS . GT:GQ:BAF:LRR 0/0:0.419872:0.0:-0.669645 +14 21623378 newrs149953865 G T . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.0:0.0936777 +14 23424338 newrs149965606 G A . PASS . GT:GQ:BAF:LRR 0/0:0.414767:0.0123677253723:0.0798318 +14 23893116 newrs147727900 C T . PASS . GT:GQ:BAF:LRR 0/0:0.437842:0.0:0.0808325 +14 24586536 newrs150144513 G A . PASS . GT:GQ:BAF:LRR 0/0:0.517166:0.0:0.0760514 +14 39543728 newrs148248798 C A . PASS . GT:GQ:BAF:LRR 0/0:0.500193:0.0:0.0514718 +14 51378470 newrs150547274 G T . PASS . GT:GQ:BAF:LRR 0/0:0.474113:0.0:0.120842 +14 51381465 newrs150701003 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.00543302297592:-0.23124 +14 52741521 newrs150364594 C T . PASS . GT:GQ:BAF:LRR 0/0:0.511023:0.0:0.0707803 +14 57949845 newrs149798976 G A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.00780492 +14 64637040 newrs148965783 G T . PASS . GT:GQ:BAF:LRR 0/0:0.505974:0.0:0.00991983 +14 64746697 newrs148022433 A G . PASS . GT:GQ:BAF:LRR 0/0:0.511232:0.0:0.0511489 +14 65252552 newrs149186357 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.125513 +14 67854084 newrs149261200 G A . PASS . GT:GQ:BAF:LRR 0/0:0.363299:0.0:-0.0932824 +14 68934972 newrs148518198 G A . PASS . GT:GQ:BAF:LRR 0/0:0.515358:0.0:0.0268868 +14 71522261 newrs149428100 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500204:0.0:-0.0479098 +14 73421171 newrs149756917 G A . PASS . GT:GQ:BAF:LRR 0/0:0.497063:0.00985968112946:-0.450622 +14 73614807 newrs149562759 G A . PASS . GT:GQ:BAF:LRR 0/0:0.505403:0.0:-0.0520427 +14 74363143 newrs150263864 G A . PASS . GT:GQ:BAF:LRR 0/0:0.511695:0.006596326828:-0.5768 +14 74443025 newrs149628087 A C . PASS . GT:GQ:BAF:LRR 0/0:0.352786:0.0200511:0.144456 +14 76186169 newrs147593414 G A . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:0.0495186 +14 77273847 newrs150078735 T G . PASS . GT:GQ:BAF:LRR 0/0:0.498132:0.0:0.000671952 +14 77793851 newrs148051919 C T . PASS . GT:GQ:BAF:LRR 0/0:0.529202:0.0:-0.0732576 +14 81366282 newrs147570461 C T . PASS . GT:GQ:BAF:LRR 0/0:0.494117:0.0:-0.025362 +14 92084075 newrs146758171 G A . PASS . GT:GQ:BAF:LRR 0/0:0.481477:0.0:0.0497337 +14 93199039 newrs150780250 C T . PASS . GT:GQ:BAF:LRR 0/0:0.263703:0.0:0.028561 +14 94752558 newrs149414832 G A . PASS . GT:GQ:BAF:LRR 0/0:0.517914:0.0:0.119721 +14 95658040 newrs150449481 G T . PASS . GT:GQ:BAF:LRR 0/0:0.411784:0.00872367620468:-0.0999293 +14 96178607 newrs149840194 G A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.0720673 +14 97342457 newrs149083861 C T . PASS . GT:GQ:BAF:LRR 0/0:0.512952:0.0:0.0249514 +14 102822107 newrs150324463 A G . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.0:0.176048 +14 105739057 newrs147262979 C T . PASS . GT:GQ:BAF:LRR 0/0:0.455851:0.0:0.278086 +15 25971098 newrs148331114 C T . PASS . GT:GQ:BAF:LRR 0/0:0.396673:0.0:-0.083423 +15 28171292 newrs149648291 G A . PASS . GT:GQ:BAF:LRR 0/0:0.499187:0.0:-0.0508315 +15 42445860 newrs150082965 T C . PASS . GT:GQ:BAF:LRR 0/0:0.518461:0.0:0.026474 +15 42622872 newrs150469926 T G . PASS . GT:GQ:BAF:LRR 0/0:0.519141:0.0:-0.0477929 +15 42684855 newrs149591108 T C . PASS . GT:GQ:BAF:LRR 0/0:0.458216:0.00720238:-1.07268 +15 42703497 newrs149095128 C A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:-0.00834184 +15 44087615 newrs150100062 A C . PASS . GT:GQ:BAF:LRR 0/0:0.409735:0.0:0.0386938 +15 44907685 newrs150434621 G A . PASS . GT:GQ:BAF:LRR 0/0:0.514317:0.00210070610046:0.0853994 +15 45454575 newrs148367370 G T . PASS . GT:GQ:BAF:LRR 0/0:0.494563:0.0147281885147:-0.514903 +15 49924440 newrs146894806 G T . PASS . GT:GQ:BAF:LRR 0/0:0.468051:0.0:0.046572 +15 50189488 newrs150777155 C T . PASS . GT:GQ:BAF:LRR 0/0:0.404719:0.0:-0.0245929 +15 59911344 newrs149782376 C T . PASS . GT:GQ:BAF:LRR 0/0:0.413539:0.00940632820129:-0.272034 +15 62202414 newrs148074630 G A . PASS . GT:GQ:BAF:LRR 0/0:0.505129:0.0:0.101693 +15 62210341 newrs149034021 G T . PASS . GT:GQ:BAF:LRR 0/0:0.51515:0.0:0.178682 +15 64701909 newrs147303485 C T . PASS . GT:GQ:BAF:LRR 0/0:0.508698:0.00782090425491:-0.597667 +15 65447166 newrs148226354 C T . PASS . GT:GQ:BAF:LRR 0/0:0.331422:0.065142095089:-0.154789 +15 66606431 newrs150541699 C T . PASS . GT:GQ:BAF:LRR 0/0:0.509273:0.00178158283234:-0.119261 +15 71302182 newrs149193315 C T . PASS . GT:GQ:BAF:LRR 0/0:0.514607:0.0:0.334199 +15 72637823 newrs147502219 T C . PASS . GT:GQ:BAF:LRR 0/0:0.50608:0.000414106:0.0405468 +15 72699035 newrs146921317 C T . PASS . GT:GQ:BAF:LRR 0/0:0.49955:0.0:-0.064992 +15 75341568 newrs149414091 C T . PASS . GT:GQ:BAF:LRR 0/0:0.51178:0.0:0.147851 +15 79220054 newrs148219875 C T . PASS . GT:GQ:BAF:LRR 0/0:0.416371:0.0:0.0682349 +15 85342440 newrs150829393 G A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.00605225563049:0.109374 +15 89847147 newrs149464307 G A . PASS . GT:GQ:BAF:LRR 0/0:0.498335:0.0:-0.264452 +15 101113900 newrs149644940 A C . PASS . GT:GQ:BAF:LRR 0/0:0.518373:0.0:-0.116189 +15 101826419 newrs150109462 G A . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:-0.0377882 +16 1827748 newrs147512809 C T . PASS . GT:GQ:BAF:LRR 0/0:0.480007:0.0:0.198985 +16 3349792 newrs150368295 G A . PASS . GT:GQ:BAF:LRR 0/0:0.499756:0.0:0.134489 +16 3807934 newrs148166625 T C . PASS . GT:GQ:BAF:LRR 0/0:0.467473:0.0375181:-0.178464 +16 8905018 newrs150719105 T C . PASS . GT:GQ:BAF:LRR 0/0:0.517556:0.00773878:-0.821826 +16 14024712 newrs150244523 T C . PASS . GT:GQ:BAF:LRR 0/0:0.831536:0.0186962:-0.0911935 +16 14028147 newrs147458778 C T . PASS . GT:GQ:BAF:LRR 0/0:0.499078:0.0:-0.00703177 +16 19653798 newrs150266526 A G . PASS . GT:GQ:BAF:LRR 0/0:0.513806:0.0:-0.0783359 +16 23767516 newrs147036175 T G . PASS . GT:GQ:BAF:LRR 0/0:0.511852:0.0152981:-0.341801 +16 28890429 newrs150403167 C T . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.00239676237106:-0.323586 +16 30017999 newrs150127737 C T . PASS . GT:GQ:BAF:LRR 0/0:0.465068:0.0:0.0318203 +16 30596538 newrs147854775 C T . PASS . GT:GQ:BAF:LRR 0/0:0.371617:0.00957775115967:0.0818028 +16 30722073 newrs149689808 A G . PASS . GT:GQ:BAF:LRR 0/0:0.290874:0.0315611:0.151619 +16 30770661 newrs150540962 A C . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.0637325 +16 31196307 newrs148758737 G A . PASS . GT:GQ:BAF:LRR 0/0:0.211313:0.0998276472092:0.00334737 +16 31418867 newrs147321998 C T . PASS . GT:GQ:BAF:LRR 0/0:0.475085:0.0:-0.25604 +16 31425870 newrs149370240 C T . PASS . GT:GQ:BAF:LRR 0/0:0.506813:0.0:0.115725 +16 47630364 newrs146634901 C T . PASS . GT:GQ:BAF:LRR 0/0:0.490858:0.0:-0.156925 +16 48180230 newrs150215788 G A . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.213641 +16 48249135 newrs150392452 C A . PASS . GT:GQ:BAF:LRR 0/0:0.506584:0.0:0.0827859 +16 48385596 newrs150743514 C T . PASS . GT:GQ:BAF:LRR 0/0:0.509666:0.0:-0.25959 +16 55608627 newrs149963829 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.053414 +16 56534926 newrs147030232 G A . PASS . GT:GQ:BAF:LRR 0/0:0.383977:0.00260961055756:0.106897 +16 66976645 newrs147925730 T C . PASS . GT:GQ:BAF:LRR 0/0:0.490665:0.0:0.0619792 +16 67226732 newrs148234724 C T . PASS . GT:GQ:BAF:LRR 0/0:0.310014:0.0:0.0547093 +16 67646025 newrs147502048 G T . PASS . GT:GQ:BAF:LRR 0/0:0.469106:0.00348073244095:0.174057 +16 67899132 newrs148843933 C T . PASS . GT:GQ:BAF:LRR 0/0:0.509894:0.0:0.204967 +16 68105011 newrs148423881 C T . PASS . GT:GQ:BAF:LRR 0/0:0.891693:0.0:-0.00990669 +16 68856057 newrs147925149 A G . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:0.180843 +16 69366616 newrs147051782 C T . PASS . GT:GQ:BAF:LRR 0/0:0.518165:0.0:0.0258739 +16 70294970 newrs146946034 G A . PASS . GT:GQ:BAF:LRR 0/0:0.473455:0.0:0.106912 +16 71319742 newrs147189785 C A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.0076838 +16 71483660 newrs147937440 G A . PASS . GT:GQ:BAF:LRR 0/0:0.432874:0.0:0.0446202 +16 72015958 newrs150292834 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500203:0.0:0.0924446 +16 78062087 newrs149263151 G A . PASS . GT:GQ:BAF:LRR 0/0:0.499127:0.0:-0.194631 +16 84012119 newrs147214689 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519052:0.0:0.156354 +16 88926138 newrs147583352 C T . PASS . GT:GQ:BAF:LRR ./.:0.0774364:0.0992125272751:0.0320451 +16 89805351 newrs149851163 C T . PASS . GT:GQ:BAF:LRR 0/0:0.516748:0.0:0.0987733 +17 263221 newrs147094351 G A . PASS . GT:GQ:BAF:LRR 0/0:0.40356:0.000976324081421:0.192712 +17 1562030 newrs147690140 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.00343453884125:-0.177816 +17 2227800 newrs147919745 A C . PASS . GT:GQ:BAF:LRR 0/0:0.336045:0.0:0.185958 +17 10304221 newrs150717297 C A . PASS . GT:GQ:BAF:LRR 0/0:0.507941:0.0:-0.452055 +17 10348553 newrs149888634 C T . PASS . GT:GQ:BAF:LRR 0/0:0.497929:0.00817453861237:-0.140879 +17 10408830 newrs150031915 T C . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:-0.1808 +17 10595189 newrs149824738 C T . PASS . GT:GQ:BAF:LRR 0/0:0.514046:0.0:0.177347 +17 17106264 newrs150565127 G A . PASS . GT:GQ:BAF:LRR 0/0:0.376958:0.0:0.202396 +17 19839690 newrs148949492 A C . PASS . GT:GQ:BAF:LRR 0/0:0.4534:0.0:-0.175886 +17 26911669 newrs149791493 C T . PASS . GT:GQ:BAF:LRR 0/0:0.231727:0.0664598345757:-0.0365607 +17 26951283 newrs148098359 G A . PASS . GT:GQ:BAF:LRR 0/0:0.487028:0.0:-0.0464276 +17 26966331 newrs146835965 A C . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.0596718 +17 27371895 newrs148923684 C T . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.117691 +17 29187450 newrs149775337 G T . PASS . GT:GQ:BAF:LRR 0/0:0.222323:0.0850291252136:-0.936643 +17 35310470 newrs146758318 C T . PASS . GT:GQ:BAF:LRR 0/0:0.346175:0.0127606391907:0.0373722 +17 35578764 newrs147589959 C T . PASS . GT:GQ:BAF:LRR 0/0:0.504503:0.0:0.103574 +17 35993449 newrs149632848 C A . PASS . GT:GQ:BAF:LRR ./.:0.133786:0.105671346188:-0.578131 +17 40725496 newrs150572842 C T . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.00196558237076:0.0363982 +17 44248642 newrs149830411 G A . PASS . GT:GQ:BAF:LRR 0/0:0.516895:0.0:-0.337851 +17 45909571 newrs146752078 T C . PASS . GT:GQ:BAF:LRR 0/0:0.412812:0.0:-0.00522992 +17 46799678 newrs150679020 A G . PASS . GT:GQ:BAF:LRR 0/0:0.412812:0.0:0.210182 +17 47700131 newrs150193528 C T . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.0:-0.00589858 +17 52991116 newrs148143284 C A . PASS . GT:GQ:BAF:LRR 0/0:0.372283:0.000627636909485:0.0788764 +17 58303400 newrs147383770 C T . PASS . GT:GQ:BAF:LRR 0/0:0.493171:0.0:-0.166292 +17 63898371 newrs147238839 G A . PASS . GT:GQ:BAF:LRR 0/0:0.43318:0.000779747962952:-0.106356 +17 66251877 newrs149406006 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.104402 +17 67014554 newrs146820712 C T . PASS . GT:GQ:BAF:LRR 0/0:0.510942:0.0:-0.317105 +17 67079352 newrs149614799 C T . PASS . GT:GQ:BAF:LRR 0/0:0.515898:0.0:-0.0328294 +17 73035125 newrs148887046 G A . PASS . GT:GQ:BAF:LRR 0/0:0.374745:0.0:0.161957 +17 73049198 newrs150354933 C T . PASS . GT:GQ:BAF:LRR 0/0:0.406248:0.0:0.162869 +17 74574836 newrs146729471 A G . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.167866 +17 78341873 newrs149974667 C T . PASS . GT:GQ:BAF:LRR 0/0:0.511852:0.0:0.162846 +17 80972329 newrs146876805 C T . PASS . GT:GQ:BAF:LRR 0/0:0.882836:0.00267112255096:-0.0563226 +18 13114210 newrs149673520 C T . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:0.0731197 +18 33754535 newrs146555723 G A . PASS . GT:GQ:BAF:LRR 0/0:0.505147:0.0:-0.36685 +18 43262283 newrs147596856 G A . PASS . GT:GQ:BAF:LRR 0/0:0.322317:0.0582450032234:0.071208 +18 47311566 newrs147811299 C T . PASS . GT:GQ:BAF:LRR 0/0:0.517677:0.0:0.160541 +18 48333089 newrs148800283 A C . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:0.075275 +18 52586573 newrs149563439 G A . PASS . GT:GQ:BAF:LRR 0/0:0.458079:0.0:0.043438 +18 61569116 newrs150189388 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.0273585 +18 77104307 newrs147932692 C T . PASS . GT:GQ:BAF:LRR 0/0:0.459337:0.0157560110092:0.0249785 +19 2853204 newrs150017916 C T . PASS . GT:GQ:BAF:LRR 0/0:0.497155:0.0:-0.0936644 +19 2877866 newrs148855297 C T . PASS . GT:GQ:BAF:LRR 0/0:0.374566:0.00668179988861:-0.344505 +19 2934107 newrs146879198 G A . PASS . GT:GQ:BAF:LRR 0/0:0.50868:0.00336682796478:0.093836 +19 6366374 newrs147589840 G A . PASS . GT:GQ:BAF:LRR 0/0:0.402133:0.0:0.247399 +19 8152712 newrs150404330 G A . PASS . GT:GQ:BAF:LRR 0/0:0.474595:0.0:-0.0923076 +19 8979212 newrs149481309 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500971:0.0:0.00342115 +19 9237120 newrs149823005 G T . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:0.106778 +19 9453655 newrs147456906 C T . PASS . GT:GQ:BAF:LRR 0/0:0.890395:0.0:0.0189498 +19 9526374 newrs146586902 G A . PASS . GT:GQ:BAF:LRR 0/0:0.487353:0.0267685651779:0.0685457 +19 10103502 newrs149888433 C T . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.147785 +19 11227666 newrs148181903 G A . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:-0.0392318 +19 12015703 newrs148289998 G A . PASS . GT:GQ:BAF:LRR 0/0:0.163365:0.0:0.0659004 +19 12298163 newrs149038305 C T . PASS . GT:GQ:BAF:LRR 0/0:0.484988:0.0:0.0977261 +19 12298190 newrs148282298 G T . PASS . GT:GQ:BAF:LRR 0/0:0.486917:0.0:0.15965 +19 12298583 newrs149571290 C T . PASS . GT:GQ:BAF:LRR 0/0:0.484934:0.0:-0.0410026 +19 12430286 newrs150045277 G A . PASS . GT:GQ:BAF:LRR 0/0:0.462629:0.0:0.0432913 +19 12460637 newrs147649018 G A . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:0.127913 +19 14748918 newrs149254238 G A . PASS . GT:GQ:BAF:LRR 0/0:0.429903:0.0:0.036748 +19 16612192 newrs148952679 C T . PASS . GT:GQ:BAF:LRR 0/0:0.465715:0.000305891036987:-0.0132468 +19 17628609 newrs148238828 C T . PASS . GT:GQ:BAF:LRR 0/0:0.498638:0.0:0.242315 +19 18423437 newrs147169736 G A . PASS . GT:GQ:BAF:LRR 0/0:0.43126:0.0:0.0932386 +19 19304942 newrs150525759 G A . PASS . GT:GQ:BAF:LRR 0/0:0.517259:0.0:-0.0574026 +19 19822451 newrs150668126 G A . PASS . GT:GQ:BAF:LRR 0/0:0.41267:0.0:0.0153763 +19 21131548 newrs150314828 A G . PASS . GT:GQ:BAF:LRR 0/0:0.264439:0.0184669:-0.246429 +19 30102847 newrs149115361 G A . PASS . GT:GQ:BAF:LRR 0/0:0.501101:0.00481688976288:-0.0204418 +19 33093028 newrs147161211 G T . PASS . GT:GQ:BAF:LRR 0/0:0.518774:0.0019456744194:0.11531 +19 33110461 newrs147123593 T G . PASS . GT:GQ:BAF:LRR 0/0:0.409766:0.0:0.128002 +19 33321545 newrs146815072 G A . PASS . GT:GQ:BAF:LRR 0/0:0.492424:0.0:-0.0308342 +19 34890477 newrs148811525 G A . PASS . GT:GQ:BAF:LRR 0/0:0.45385:0.0:0.0267558 +19 35251195 newrs150001961 G A . PASS . GT:GQ:BAF:LRR 0/0:0.498791:0.00469571352005:-0.38209 +19 35979712 newrs149292016 G A . PASS . GT:GQ:BAF:LRR 0/0:0.405942:0.0:0.0529032 +19 36636905 newrs148900101 C T . PASS . GT:GQ:BAF:LRR 0/0:0.514213:0.0:0.0542241 +19 37005949 newrs149550734 G T . PASS . GT:GQ:BAF:LRR 0/0:0.499997:0.0:0.165992 +19 37309679 newrs147371360 G A . PASS . GT:GQ:BAF:LRR 0/0:0.467707:0.0:-0.0473625 +19 37310282 newrs147290327 G A . PASS . GT:GQ:BAF:LRR 0/0:0.261638:0.0198075771332:-0.104442 +19 37677067 newrs150349013 G A . PASS . GT:GQ:BAF:LRR 0/0:0.507021:0.00143718719482:-0.0305527 +19 37853304 newrs149469668 C T . PASS . GT:GQ:BAF:LRR 0/0:0.516052:0.0:-0.11237 +19 38055670 newrs149435363 C A . PASS . GT:GQ:BAF:LRR 0/0:0.495671:0.00357013940811:0.205529 +19 38160389 newrs147935289 C A . PASS . GT:GQ:BAF:LRR ./.:0.00387779:0.192010521889:-0.153111 +19 38230107 newrs149484261 G T . PASS . GT:GQ:BAF:LRR 0/0:0.494433:0.0:0.0136336 +19 38945887 newrs147723844 A G . PASS . GT:GQ:BAF:LRR 0/0:0.711998:0.0:0.145316 +19 39034005 newrs148399313 G A . PASS . GT:GQ:BAF:LRR 0/0:0.439902:0.0:0.0461478 +19 39076780 newrs146876145 C T . PASS . GT:GQ:BAF:LRR 0/0:0.482913:0.00675463676453:-0.262015 +19 40197274 newrs150238702 C A . PASS . GT:GQ:BAF:LRR 0/0:0.32364:0.0:-0.00544655 +19 40580545 newrs149702621 G A . PASS . GT:GQ:BAF:LRR 0/0:0.360361:0.0:-0.150464 +19 40580629 newrs147947129 G A . PASS . GT:GQ:BAF:LRR 0/0:0.3047:0.0:-0.0823699 +19 41920067 newrs149899007 G A . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:0.0918607 +19 42190820 newrs150439369 C A . PASS . GT:GQ:BAF:LRR 0/0:0.381426:0.0217183828354:-0.200623 +19 43699204 newrs147584129 C A . PASS . GT:GQ:BAF:LRR 0/0:0.461736:0.0:-0.0188369 +19 43762499 newrs150777161 C T . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:-0.0222313 +19 43771960 newrs146901255 G A . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:-0.253375 +19 44280789 newrs147965350 C T . PASS . GT:GQ:BAF:LRR 0/0:0.474791:0.0382894277573:0.0832743 +19 44500621 newrs147279924 T G . PASS . GT:GQ:BAF:LRR 0/0:0.517605:0.0:-0.30084 +19 49341353 newrs150707206 G A . PASS . GT:GQ:BAF:LRR 0/0:0.499477:0.0:-0.0328186 +19 58099976 newrs148725359 C T . PASS . GT:GQ:BAF:LRR 0/0:0.196519:0.0:0.0264718 +19 58146047 newrs147342045 G A . PASS . GT:GQ:BAF:LRR 0/0:0.506865:0.0:-0.0435322 +19 58578441 newrs148932599 G T . PASS . GT:GQ:BAF:LRR 0/0:0.410472:0.0:-0.202507 +20 1961587 newrs149872114 G T . PASS . GT:GQ:BAF:LRR 0/0:0.519086:0.0:-0.151775 +20 3210383 newrs150571742 T C . PASS . GT:GQ:BAF:LRR 0/0:0.463099:0.0:0.034672 +20 8626828 newrs148738915 C T . PASS . GT:GQ:BAF:LRR 0/0:0.503645:0.0:-0.656115 +20 10386055 newrs149051148 C T . PASS . GT:GQ:BAF:LRR 0/0:0.823464:0.0:-0.066093 +20 10393273 newrs147704542 A G . PASS . GT:GQ:BAF:LRR 0/0:0.51201:0.0:-0.13239 +20 10582468 newrs148856218 G A . PASS . GT:GQ:BAF:LRR 0/0:0.518749:0.0:-0.139811 +20 16359919 newrs148283912 G A . PASS . GT:GQ:BAF:LRR 0/0:0.436915:0.0:0.011523 +20 16488602 newrs147318741 C T . PASS . GT:GQ:BAF:LRR 0/0:0.44896:0.0:-0.0658218 +20 20180478 newrs147638085 C T . PASS . GT:GQ:BAF:LRR 0/0:0.43418:0.0:-0.314772 +20 25484742 newrs150265900 T C . PASS . GT:GQ:BAF:LRR 0/0:0.361595:0.0:-0.229587 +20 29965124 newrs146735308 G T . PASS . GT:GQ:BAF:LRR 0/0:0.456015:0.0:0.0810949 +20 30616808 newrs149235259 C T . PASS . GT:GQ:BAF:LRR 0/0:0.449635:0.0:0.0314867 +20 30904102 newrs149015672 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.00775563716888:-0.294049 +20 31388016 newrs146981624 T C . PASS . GT:GQ:BAF:LRR 0/0:0.348161:0.000381047:0.0353587 +20 31572946 newrs147686372 G A . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:0.0245875 +20 31954730 newrs148992921 G A . PASS . GT:GQ:BAF:LRR 0/0:0.412879:0.0:-0.0692842 +20 35526320 newrs149846637 G A . PASS . GT:GQ:BAF:LRR 0/0:0.506012:0.00400620698929:0.0680538 +20 36953197 newrs150749170 C T . PASS . GT:GQ:BAF:LRR 0/0:0.494166:0.0:-0.396903 +20 43629072 newrs148138374 C T . PASS . GT:GQ:BAF:LRR 0/0:0.529569:0.0:-0.112961 +20 43837202 newrs147667060 C T . PASS . GT:GQ:BAF:LRR 0/0:0.497983:0.0:-0.127842 +20 44141410 newrs148191315 G A . PASS . GT:GQ:BAF:LRR 0/0:0.872238:0.0:0.0923713 +20 49576632 newrs149569136 C A . PASS . GT:GQ:BAF:LRR 0/0:0.484587:0.0:-0.036793 +20 53266980 newrs148201917 C T . PASS . GT:GQ:BAF:LRR 0/0:0.410906:0.00440800189972:0.0526855 +20 62851132 newrs150660744 G T . PASS . GT:GQ:BAF:LRR 0/0:0.376958:0.0:0.0333837 +21 31538770 newrs148594408 G A . PASS . GT:GQ:BAF:LRR 0/0:0.518862:0.0:-0.0526677 +21 32119310 newrs147814118 G A . PASS . GT:GQ:BAF:LRR 0/0:0.512012:0.0:0.0954213 +21 34950699 newrs147521584 C T . PASS . GT:GQ:BAF:LRR 0/0:0.508082:0.0:-0.104971 +21 35742857 newrs148968498 G A . PASS . GT:GQ:BAF:LRR 0/0:0.482174:0.0:-0.297359 +21 37408510 newrs148061279 G A . PASS . GT:GQ:BAF:LRR 0/0:0.461888:0.00132811069489:0.0176279 +21 38128952 newrs149399432 C T . PASS . GT:GQ:BAF:LRR 0/0:0.429459:0.0:0.092287 +21 42821222 newrs148192027 G A . PASS . GT:GQ:BAF:LRR 0/0:0.503574:0.0:-0.157748 +21 43862591 newrs148203332 C T . PASS . GT:GQ:BAF:LRR 0/0:0.454809:0.0:0.0516431 +21 44323380 newrs148055450 C A . PASS . GT:GQ:BAF:LRR 0/0:0.5153:0.00846242904663:0.167604 +21 46314884 newrs149804560 A G . PASS . GT:GQ:BAF:LRR 0/0:0.500064:0.0:0.142767 +22 20907430 newrs149792139 A C . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.0194699 +22 26114280 newrs148927409 C T . PASS . GT:GQ:BAF:LRR 0/0:0.417444:0.0:0.108142 +22 29130534 newrs149991239 G T . PASS . GT:GQ:BAF:LRR 0/0:0.506522:0.0:0.0857932 +22 29456783 newrs146955915 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.377919 +22 32792056 newrs146836672 T C . PASS . GT:GQ:BAF:LRR 0/0:0.472745:0.0:0.0513183 +22 36653372 newrs149411999 C T . PASS . GT:GQ:BAF:LRR 0/0:0.423935:0.0:-0.022094 +22 39148627 newrs148700122 G A . PASS . GT:GQ:BAF:LRR 0/0:0.494921:0.0:0.145634 +22 41188676 newrs147898473 C T . PASS . GT:GQ:BAF:LRR 0/0:0.367053:0.00573420524597:0.0638442 +22 41305124 newrs149609214 A G . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:-0.0169839 +22 41605795 newrs146730690 G A . PASS . GT:GQ:BAF:LRR 0/0:0.410227:0.0:0.0657953 +22 41863452 newrs148099525 G A . PASS . GT:GQ:BAF:LRR 0/0:0.529569:0.0:-0.184435 +22 43464415 newrs146662174 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:0.195691 +X 3241377 newrs150681202 C T . PASS . GT:GQ:BAF:LRR 0:0.401561:0.0:0.0395558 +X 44950109 newrs148188315 A G . PASS . GT:GQ:BAF:LRR 0:0.513279:0.0:-0.202387 +X 62917005 newrs150129110 G A . PASS . GT:GQ:BAF:LRR 0:0.513773:0.0:0.0654194 +X 63445212 newrs148346736 G A . PASS . GT:GQ:BAF:LRR 0:0.419945:0.0:-0.0193036 +X 73524476 newrs149628222 C A . PASS . GT:GQ:BAF:LRR 0:0.508385:0.0:-0.213667 +X 101091706 newrs146841797 C A . PASS . GT:GQ:BAF:LRR 0:0.388738:0.00501638650894:0.0018265 +X 106331799 newrs149164060 C T . PASS . GT:GQ:BAF:LRR 0:0.464871:0.0:0.00401862 +X 111698143 newrs148205998 C T . PASS . GT:GQ:BAF:LRR 0:0.516643:0.0:0.0937407 +X 134987551 newrs147659975 C T . PASS . GT:GQ:BAF:LRR .:0.0271973:0.855071529746:-1.02109 +X 135095107 newrs149044510 C T . PASS . GT:GQ:BAF:LRR 0:0.517983:0.00356465578079:-0.024875 +X 152835147 newrs147874519 C T . PASS . GT:GQ:BAF:LRR 0:0.386838:0.0:0.0554279 +X 153642450 newrs146934311 T C . PASS . GT:GQ:BAF:LRR 0:0.632201:0.0:-1.27112 +X 153997508 newrs146700772 A C . PASS . GT:GQ:BAF:LRR 0:0.446295:0.0:-0.089962 +X 154159071 newrs149853218 A C . PASS . GT:GQ:BAF:LRR 0:0.831019:0.0:0.0311412 +MT 125 200610-102 T C . PASS . GT:GQ:BAF:LRR 0:0.446263:0.0:0.115358 +MT 212 200610-104 T C . PASS . GT:GQ:BAF:LRR 0:0.398159:0.0:0.295681 +MT 236 200610-105 T C . PASS . GT:GQ:BAF:LRR 0:0.648628:0.0:0.544095 +MT 482 200610-107 T C . PASS . GT:GQ:BAF:LRR 0:0.812968:0.0:-0.145008 +MT 3396 200610-111 T C . PASS . GT:GQ:BAF:LRR 0:0.666947:0.0:0.309391 +MT 3644 200610-112 T C . PASS . GT:GQ:BAF:LRR 0:0.361595:0.0:0.25045 +MT 3645 200610-113 T C . PASS . GT:GQ:BAF:LRR 0:0.374745:0.0:0.28055 +MT 3826 200610-114 T C . PASS . GT:GQ:BAF:LRR 0:0.374745:0.0:0.169423 +MT 5048 200610-119 T C . PASS . GT:GQ:BAF:LRR 0:0.35256:0.0:0.312317 +MT 5108 200610-120 T C . PASS . GT:GQ:BAF:LRR 0:0.310474:0.0:0.371067 +MT 6248 200610-121 T C . PASS . GT:GQ:BAF:LRR 0:0.361595:0.0:0.329944 +MT 6392 200610-123 T C . PASS . GT:GQ:BAF:LRR 0:0.480041:0.0:-0.358642 +MT 7861 200610-127 T C . PASS . GT:GQ:BAF:LRR 0:0.242924:0.00810775:0.191825 +MT 7870 200610-128 T C . PASS . GT:GQ:BAF:LRR 0:0.312218:0.0:0.465192 +MT 7972 200610-13 A G . PASS . GT:GQ:BAF:LRR 0:0.335269:0.0462774:-0.103078 +MT 8502 200610-14 A G . PASS . GT:GQ:BAF:LRR 0:0.500205:0.0:-0.00160825 +MT 10118 200610-133 T C . PASS . GT:GQ:BAF:LRR 0:0.376958:0.0:0.367449 +MT 12121 200610-136 T C . PASS . GT:GQ:BAF:LRR 0:0.376958:0.0:0.15068 +MT 12285 200610-137 T C . PASS . GT:GQ:BAF:LRR 0:0.440272:0.0:0.451548 +MT 13215 200610-138 T C . PASS . GT:GQ:BAF:LRR 0:0.384898:0.0:0.692635 +MT 15172 200610-100 G A . PASS . GT:GQ:BAF:LRR 0:0.219084:0.0143872499466:-0.0584293 +MT 15514 200610-143 T C . PASS . GT:GQ:BAF:LRR 0:0.648628:0.0:0.163682 +MT 16217 200610-146 T C . PASS . GT:GQ:BAF:LRR 0:0.436944:0.00950987:-0.00556835 diff --git a/tests/test_class.py b/tests/test_class.py index 8a9f290..80792f0 100644 --- a/tests/test_class.py +++ b/tests/test_class.py @@ -78,6 +78,13 @@ def test(self): self.run_regression(command, output_vcf, os.path.join(SCRIPT_DIR, "data", "RegressionAux", "output", "output.vcf")) os.remove(output_vcf) +class RegressionIncludeAttributes(Regression): + def test(self): + output_vcf = tempfile.mktemp(suffix=".vcf") + command = [sys.executable, self.get_script(), "--genome-fasta-file", self.get_genome(), "--manifest-file", os.path.join(SCRIPT_DIR, "data", "small_manifest.bpm"), "--gtc-paths", os.path.join(SCRIPT_DIR, "data", "RegressionIncludeAttributes", "input", "201142750001_R01C01.gtc"), "--output-vcf-path", output_vcf, "--disable-genome-cache", "--skip-indels", "--include-attributes", "GT", "GQ", "BAF", "LRR"] + self.run_regression(command, output_vcf, os.path.join(SCRIPT_DIR, "data", "RegressionIncludeAttributes", "output", "output.vcf")) + os.remove(output_vcf) + class TestSourceSequence(unittest.TestCase): def test_source_sequence_split(self): (five_prime, indel, three_prime) = IndelSourceSequence.split_source_sequence("ACGT[-/ATAT]GGTA") From 1534ff0ce03d5911d3fdbf08535de219bad1b102 Mon Sep 17 00:00:00 2001 From: Jake Zieve Date: Fri, 10 May 2019 13:50:13 -0700 Subject: [PATCH 27/34] Adds support for indels and fixes a bug with an assertion --- BAlleleFreqFormat.py | 48 +++++++++++++++++++++++++++++++++++--------- 1 file changed, 38 insertions(+), 10 deletions(-) diff --git a/BAlleleFreqFormat.py b/BAlleleFreqFormat.py index 190a939..c2326e0 100644 --- a/BAlleleFreqFormat.py +++ b/BAlleleFreqFormat.py @@ -2,7 +2,7 @@ from IlluminaBeadArrayFiles import RefStrand import numpy as np -REVERSE_COMPLIMENT = {"A": "T", "T": "A", "G": "C", "C": "G"} +REVERSE_COMPLIMENT = {"A": "T", "T": "A", "G": "C", "C": "G", "I": "I", "D": "D"} def extract_alleles_from_snp_string(snp_string): @@ -16,8 +16,8 @@ def extract_alleles_from_snp_string(snp_string): allele1 (string), allele2 (string) """ (allele1, allele2) = snp_string[1:4].split("/") - # assert allele1 in "ATGC", "allele %r is invalid (expected A,T,G,C)" % allele1 - # assert allele2 in "ATGC", "allele %r is invalid (expected A,T,G,C)" % allele2 + assert allele1 in "ATGCID", "allele %r is invalid (expected A,T,G,C,I,D)" % allele1 + assert allele2 in "ATGCID", "allele %r is invalid (expected A,T,G,C,I,D)" % allele2 return allele1, allele2 @@ -38,6 +38,30 @@ def normalize_alleles_by_strand(snp_string): return REVERSE_COMPLIMENT[allele1], REVERSE_COMPLIMENT[allele2] +def convert_indel_alleles(snp_string, vcf_record): + """ + Splits SNP string into tuple of individual alleles and + converts to actual insertion/deletion alleles from the reference + + Args: snp_string (string): allele string of the format + [I/D] or [D/I] + + Returns: + allele1 (string), allele2 (string) + """ + # get alleles as tuple, we only need allele1 because if its "I" we can assume allele2 will be "D" and vice-versa + allele1, _ = extract_alleles_from_snp_string(snp_string) + + assert len(vcf_record.ALT) == 1, "Cannot convert indel for BAF with multiple ALT alleles" + alt_allele = str(vcf_record.ALT[0]) + ref_allele = vcf_record.REF + # Assuming whichever sequence is smaller is the deletion and the larger is the insertion + assert len(alt_allele) > len(ref_allele) or len(ref_allele) > len(alt_allele), "REF allele %r and ALT allele %r same length, cannot determine insertion or deletion" % (ref_allele, alt_allele) + deletion_allele, insertion_allele = (alt_allele, ref_allele) if len(alt_allele) < len(ref_allele) else (ref_allele, alt_allele) + if allele1 == "I": + return insertion_allele, deletion_allele + return deletion_allele, insertion_allele + class BAlleleFreqFormat(object): """ Generate b allele frequency format information for VCF @@ -74,20 +98,24 @@ def generate_sample_format_info(self, bpm_records, vcf_record, sample_name): if len(vcf_record.ALT) > 1: return "." for i in range(len(bpm_records)): - snp = bpm_records[i].snp - strand = bpm_records[i].ref_strand - - idx = bpm_records[i].index_num + bpm_record = bpm_records[i] + snp = bpm_record.snp + strand = bpm_record.ref_strand + idx = bpm_record.index_num b_allele_freq = self._b_allele_freq[idx] - # if second (minus) strand, normalize strand - if strand == RefStrand.Minus: + + # if indel, convert to actual ref and alt sequences + if bpm_record.is_indel(): + allele1, allele2 = convert_indel_alleles(snp, vcf_record) + # if 2/minus strand, normalize strand + elif strand == RefStrand.Minus: allele1, allele2 = normalize_alleles_by_strand(snp) else: allele1, allele2 = extract_alleles_from_snp_string(snp) # normalize to reference allele ref_allele = vcf_record.REF - assert allele1 == ref_allele or allele2 == ref_allele + assert allele1 == ref_allele or allele2 == ref_allele, "allele1: %r or allele2 %r do not match ref: %r" % (allele1, allele2, ref_allele) # if allele1 is reference, then B allele is correct if allele1 == ref_allele: b_allele_freq_list.append(b_allele_freq) From 1d2879cb8c01924d551ec489f7add29210b5ae01 Mon Sep 17 00:00:00 2001 From: Jake Zieve Date: Fri, 10 May 2019 13:53:34 -0700 Subject: [PATCH 28/34] Updates regression for include attributes to allow indels --- .../output/output.vcf | 984 ++++++++++++++++++ tests/test_class.py | 2 +- 2 files changed, 985 insertions(+), 1 deletion(-) diff --git a/tests/data/RegressionIncludeAttributes/output/output.vcf b/tests/data/RegressionIncludeAttributes/output/output.vcf index d7ccf49..cd8c501 100644 --- a/tests/data/RegressionIncludeAttributes/output/output.vcf +++ b/tests/data/RegressionIncludeAttributes/output/output.vcf @@ -31,43 +31,81 @@ ##contig= ##contig= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12753 +1 1158675 1KG_1_1158675 C CCTT . PASS . GT:GQ:BAF:LRR 0/0:0.437028:0.0:0.167821 1 3542422 newrs148462952 G T . PASS . GT:GQ:BAF:LRR 0/0:0.470694:0.0375163555145:-0.302043 1 3673329 newrs150537276 G T . PASS . GT:GQ:BAF:LRR 0/0:0.440959:0.000932812690735:0.0373033 1 6592659 newrs146978611 G A . PASS . GT:GQ:BAF:LRR 0/0:0.459709:0.0:-0.0163632 +1 6727802 1KG_1_6727802 T TTC . PASS . GT:GQ:BAF:LRR 0/0:0.386117:0.0:0.0770388 1 9083101 newrs148511942 G A . PASS . GT:GQ:BAF:LRR 0/0:0.517935:0.0:-0.468414 +1 11193226 1KG_1_11193226 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.344823:0.0260934:-0.102067 1 11855351 newrs147750177 C A . PASS . GT:GQ:BAF:LRR 0/0:0.437521:0.0:0.0952104 +1 11893660 1KG_1_11893660 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.496269:0.0:-0.157595 +1 12066749 1KG_1_12066749 T TGGTCAGTGACCA . PASS . GT:GQ:BAF:LRR 0/0:0.425916:0.0117156:-0.342089 +1 12343587 1KG_1_12343587 A AT . PASS . GT:GQ:BAF:LRR 0/0:0.499107:0.0:0.0759172 +1 12632789 1KG_1_12632789 G GGGA . PASS . GT:GQ:BAF:LRR 0/0:0.195181:0.0:0.0362504 +1 12711251 1KG_1_12711251 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.399567:0.0:-0.20747 1 12815677 newrs147495703 C T . PASS . GT:GQ:BAF:LRR 0/0:0.416216:0.00122195482254:-0.00691045 +1 14106394 1KG_1_14106394 A ACTC . PASS . GT:GQ:BAF:LRR 0/0:0.812843:0.0576592:-1.11886 1 15886141 newrs148404423 C T . PASS . GT:GQ:BAF:LRR 0/0:0.507022:0.0:-0.134808 +1 16259647 1KG_1_16259647 T TAGC . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.0567206 1 17355095 newrs150542357 G A . PASS . GT:GQ:BAF:LRR 0/0:0.386914:0.0:-0.027109 1 17606926 newrs148561129 T C . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.000139713:-0.216337 +1 19518754 1KG_1_19518754 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.403464:0.0:-0.339294 +1 23735172 1KG_1_23735172 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.435554:0.0:-0.0146636 1 23761066 newrs147652133 G A . PASS . GT:GQ:BAF:LRR 0/0:0.450165:0.0:0.0327107 +1 24189631 1KG_1_24189631 C CAA . PASS . GT:GQ:BAF:LRR 0/0:0.413705:0.0:0.061153 +1 24687454 1KG_1_24687454 TACTG T . PASS . GT:GQ:BAF:LRR 0/0:0.500095:0.0288781:-0.14153 1 24706142 newrs149733917 C T . PASS . GT:GQ:BAF:LRR 0/0:0.495026:0.0:0.134454 1 25569197 newrs149585550 C T . PASS . GT:GQ:BAF:LRR 0/0:0.518814:0.0:-0.0799513 +1 26299200 1KG_1_26299200 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.181542 1 27210706 newrs149255985 G A . PASS . GT:GQ:BAF:LRR 0/0:0.518421:0.0:-0.00447297 +1 28564457 1KG_1_28564457 C CAGA . PASS . GT:GQ:BAF:LRR 0/0:0.430932:0.0:0.0858541 +1 28864489 1KG_1_28864489 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.00636863708496:0.113786 +1 29606117 1KG_1_29606117 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.500149:0.0:-0.76854 1 32686800 newrs146923152 T C . PASS . GT:GQ:BAF:LRR 0/0:0.400206:0.0:-0.0655664 +1 36921845 1KG_1_36921845 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.456386:0.0:0.0769019 1 38005758 newrs150740046 C A . PASS . GT:GQ:BAF:LRR 0/0:0.422011:0.0:0.140212 1 38041298 newrs148032409 G A . PASS . GT:GQ:BAF:LRR 0/0:0.458729:0.00232577323914:0.052806 +1 39798401 1KG_1_39798401 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.477806:0.0180059671402:-0.693108 +1 39798630 1KG_1_39798630 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.401901:0.112172007561:-1.07989 1 39824545 newrs148300193 G A . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.309027 +1 40129103 1KG_1_40129103 A AGG . PASS . GT:GQ:BAF:LRR 0/0:0.444258:0.00113941:-0.322148 1 40546155 newrs148412181 C T . PASS . GT:GQ:BAF:LRR 0/0:0.361595:0.0:0.0901604 +1 40737593 1KG_1_40737593 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.476047:0.0:-0.156399 1 40874410 newrs146684027 C T . PASS . GT:GQ:BAF:LRR 0/0:0.471341:0.0:0.154208 1 40928587 newrs148910082 G T . PASS . GT:GQ:BAF:LRR 0/0:0.516679:0.0:0.136911 +1 40980308 1KG_1_40980308 T TA . PASS . GT:GQ:BAF:LRR 0/0:0.876878:0.00802302360535:-0.00164552 1 41012572 newrs149604550 G T . PASS . GT:GQ:BAF:LRR 0/0:0.492112:0.0:-1.01427 +1 41481863 1KG_1_41481863 A ATCT . PASS . GT:GQ:BAF:LRR 0/0:0.50463:0.0:-0.320432 1 42671432 newrs148054297 C T . PASS . GT:GQ:BAF:LRR 0/0:0.517206:0.0:0.00124651 1 43119487 newrs147914563 A C . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.268466 +1 43263770 1KG_1_43263770 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.433462:0.0298765:-0.534554 1 44257821 newrs148531289 G A . PASS . GT:GQ:BAF:LRR 0/0:0.500078:0.0:0.0420391 1 45479585 newrs150702733 C T . PASS . GT:GQ:BAF:LRR 0/0:0.487346:0.0120387077332:-0.117675 1 46032360 newrs150476930 G A . PASS . GT:GQ:BAF:LRR 0/0:0.502872:0.0:0.182893 +1 47048942 1KG_1_47048942 G GCTT . PASS . GT:GQ:BAF:LRR 0/0:0.483202:0.0122318267822:-0.126868 1 47101568 newrs149829714 C A . PASS . GT:GQ:BAF:LRR 0/0:0.411203:0.0:0.0375702 1 47149049 newrs149160356 G T . PASS . GT:GQ:BAF:LRR 0/0:0.468272:0.0:-0.0719191 1 47571800 newrs149156333 G A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:-0.0608993 1 48771458 newrs150721160 C A . PASS . GT:GQ:BAF:LRR 0/0:0.511883:0.0:0.332273 1 53153451 newrs149085843 G A . PASS . GT:GQ:BAF:LRR 0/0:0.336045:0.00500947237015:-0.0643592 +1 53236781 1KG_1_53236781 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.480092:0.00988388061523:-0.233278 +1 53370388 1KG_1_53370388 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.477229:0.0:-0.475709 +1 54433433 1KG_1_54433433 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.453371:0.0:0.104037 1 55277538 newrs148698352 G A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.161932 1 55307307 newrs147428017 G A . PASS . GT:GQ:BAF:LRR 0/0:0.467145:0.0:0.0115098 1 57207829 newrs148260034 C T . PASS . GT:GQ:BAF:LRR 0/0:0.516963:0.0:-0.0790384 1 57422472 newrs150022116 G A . PASS . GT:GQ:BAF:LRR 0/0:0.403158:0.0:0.0673411 +1 57476862 1KG_1_57476862 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.515291:0.0:0.00701717 1 57610963 newrs148293352 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.00695061683655:0.132613 +1 59248649 1KG_1_59248649 T TGGGGTTACTG . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:-0.0392026 +1 60106962 1KG_1_60106962 G GATATCTGT . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.143362 1 60373471 newrs150250306 G T . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.0800018 +1 62921149 1KG_1_62921149 A ATAGT . PASS . GT:GQ:BAF:LRR 0/0:0.517908:0.0:0.328952 +1 63063592 1KG_1_63063592 GAACTC G . PASS . GT:GQ:BAF:LRR 0/0:0.512453:0.0:0.00459407 +1 63299729 1KG_1_63299729 T TTG . PASS . GT:GQ:BAF:LRR 0/0:0.518873:0.0:0.191342 +1 63920634 1KG_1_63920634 A AT . PASS . GT:GQ:BAF:LRR 0/0:0.510673:0.0:0.208747 +1 67450498 1KG_1_67450498 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.502528:0.0:0.404401 1 70761813 newrs150473953 T C . PASS . GT:GQ:BAF:LRR 0/0:0.510061:0.0:0.0189942 1 76205797 newrs148260275 T C . PASS . GT:GQ:BAF:LRR 0/0:0.501148:0.0:-0.655021 1 76211574 newrs149678400 C A . PASS . GT:GQ:BAF:LRR 0/0:0.516476:0.00524163246155:0.097089 @@ -75,35 +113,57 @@ 1 76226946 newrs150310121 G A . PASS . GT:GQ:BAF:LRR 0/0:0.517069:0.0:0.176186 1 79094069 newrs147126504 C T . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.00148546695709:-0.410639 1 85431301 newrs148979230 G T . PASS . GT:GQ:BAF:LRR 0/0:0.510376:0.0:0.0263765 +1 87025657 newrs148031684 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.485383:0.0:-0.30872 +1 87181529 1KG_1_87181529 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.497042:0.0:-0.0263967 1 89520397 newrs150057659 C A . PASS . GT:GQ:BAF:LRR 0/0:0.517815:0.0157161951065:-0.385665 1 89616216 newrs150032762 C T . PASS . GT:GQ:BAF:LRR 0/0:0.489807:0.0:0.0995271 1 89734412 newrs147816214 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.0986295 1 90478723 newrs149719190 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500107:0.000285029411316:-0.0801836 +1 91180300 1KG_1_91180300 T TTCC . PASS . GT:GQ:BAF:LRR 0/0:0.511852:0.0:-0.154091 +1 93159881 1KG_1_93159881 T TGC . PASS . GT:GQ:BAF:LRR 0/0:0.462962:0.0:-0.226649 +1 94502312 1KG_1_94502312 T TGAATCA . PASS . GT:GQ:BAF:LRR 0/0:0.519014:0.0:-0.11518 1 94578619 newrs150452677 G A . PASS . GT:GQ:BAF:LRR 0/0:0.376958:0.0:-0.0854469 1 97915724 newrs147601618 A G . PASS . GT:GQ:BAF:LRR 0/0:0.467283:0.000459123:0.0661342 +1 100177980 1KG_1_100177980 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.480417:0.0:0.0311526 +1 108681808 1KG_1_108681808 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.403438:0.0:0.127132 1 108697712 newrs147531188 G A . PASS . GT:GQ:BAF:LRR 0/0:0.49223:0.0:-0.390987 1 109315442 newrs148829120 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519554:0.0:-0.134188 1 109358861 newrs149826017 G A . PASS . GT:GQ:BAF:LRR 0/0:0.517514:0.0:0.0669972 +1 109440678 1KG_1_109440678 C CAGA . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:0.0526934 1 110280079 newrs149969876 C T . PASS . GT:GQ:BAF:LRR 0/0:0.494467:0.0:-0.353095 +1 110655430 1KG_1_110655430 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.816245:0.0532484054565:-0.324624 1 111783947 newrs149638402 A C . PASS . GT:GQ:BAF:LRR 0/0:0.471613:0.0:-0.0765495 1 112020623 newrs147652304 G T . PASS . GT:GQ:BAF:LRR 0/0:0.399274:0.0:0.0895069 1 113253230 newrs147305772 G A . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.000909924507141:0.200122 +1 113933669 1KG_1_113933669 T TGAA . PASS . GT:GQ:BAF:LRR 0/0:0.503051:0.0:-0.180906 1 114443858 newrs149705131 C T . PASS . GT:GQ:BAF:LRR 0/0:0.508243:0.0:0.0274177 1 114450747 newrs150374247 C T . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:0.0562876 1 114641717 newrs149899868 G A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0370052456856:0.0423265 +1 115218558 1KG_1_115218558 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.477359:0.0:0.0269975 +1 115258741 1KG_1_115258741 A ACACCACCTGCTCCAAC . PASS . GT:GQ:BAF:LRR 0/0:0.210039:0.0910362:-0.268757 +1 115527488 1KG_1_115527488 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.470324:0.0:-0.72102 1 117620549 newrs150482379 C T . PASS . GT:GQ:BAF:LRR 0/0:0.495602:0.0:0.100861 +1 117644041 1KG_1_117644041 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.497906:0.0:-0.0793321 1 118494704 newrs149832695 G A . PASS . GT:GQ:BAF:LRR 0/0:0.443041:0.0:0.174005 1 120277390 newrs149128100 G A . PASS . GT:GQ:BAF:LRR 0/0:0.469331:0.0404487848282:-0.265325 +1 145562155 1KG_1_145562155 A AAGG . PASS . GT:GQ:BAF:LRR 0/0:0.511181:0.0:-0.112868 +1 146687322 1KG_1_146687322 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.513792:0.0:-0.321797 1 146765310 newrs149664186 C T . PASS . GT:GQ:BAF:LRR 0/0:0.374745:0.0:0.016838 +1 150201529 1KG_1_150201529 A AT . PASS . GT:GQ:BAF:LRR 0/0:0.517674:0.00350773334503:0.0798332 1 150236277 newrs150286906 G A . PASS . GT:GQ:BAF:LRR 0/0:0.454041:0.0:0.190005 +1 150255715 1KG_1_150255715 A ACT . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.00201563:0.0398311 1 150679139 newrs150156011 G A . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:-0.192496 1 150680779 newrs147466313 A C . PASS . GT:GQ:BAF:LRR 0/0:0.470807:0.0:-0.234179 1 150935195 newrs148336558 T C . PASS . GT:GQ:BAF:LRR 0/0:0.450795:0.0:-0.0358204 +1 150938672 1KG_1_150938672 T TA . PASS . GT:GQ:BAF:LRR 0/0:0.493938:0.00244629383087:0.0817012 1 151774172 newrs149393439 G A . PASS . GT:GQ:BAF:LRR 0/0:0.498079:0.0:0.302621 1 152323551 newrs150581091 A C . PASS . GT:GQ:BAF:LRR 0/0:0.49567:0.0:-0.191636 1 152325692 newrs148445702 G A . PASS . GT:GQ:BAF:LRR 0/0:0.483939:0.00202637910843:0.125953 1 152882541 newrs149812110 C T . PASS . GT:GQ:BAF:LRR 0/0:0.468768:0.0:-0.152137 +1 153641026 1KG_1_153641026 A ATTT . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0141401290894:-0.390252 +1 153984801 1KG_1_153984801 T TGAG . PASS . GT:GQ:BAF:LRR 0/0:0.467212:0.00447989:-0.0956315 1 154247447 newrs149409924 G A . PASS . GT:GQ:BAF:LRR 0/0:0.487384:0.0:0.0326374 +1 154931796 1KG_1_154931796 A AGAG . PASS . GT:GQ:BAF:LRR 0/0:0.419621:0.0:0.0894026 1 154956201 newrs149321878 C T . PASS . GT:GQ:BAF:LRR 0/0:0.441128:0.0:0.105524 1 155001836 newrs149078228 G T . PASS . GT:GQ:BAF:LRR 0/0:0.496628:0.0:-0.277777 1 155170349 newrs147564978 G T . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.0:0.0712592 @@ -111,135 +171,281 @@ 1 156316558 newrs150769956 G A . PASS . GT:GQ:BAF:LRR 0/0:0.469558:0.0:-0.058503 1 156563199 newrs147197432 G A . PASS . GT:GQ:BAF:LRR 0/0:0.505226:0.00189685821533:-0.681026 1 156641687 newrs148343241 G A . PASS . GT:GQ:BAF:LRR 0/0:0.514253:0.0:-0.522988 +1 157504353 1KG_1_157504353 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.696018:0.0114594:0.0236513 +1 157740427 1KG_1_157740427 C CAG . PASS . GT:GQ:BAF:LRR 0/0:0.513794:0.0:-0.0670771 1 158151902 newrs149673076 C T . PASS . GT:GQ:BAF:LRR 0/0:0.898959:0.0:0.0407713 +1 158436285 1KG_1_158436285 C CTTAG . PASS . GT:GQ:BAF:LRR 0/0:0.409735:0.0:0.0684199 +1 158517832 1KG_1_158517832 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.363792:0.0:-0.112051 1 158912073 newrs150672460 C T . PASS . GT:GQ:BAF:LRR 0/0:0.464363:0.0170405507088:-0.459974 1 159779984 newrs148078638 T G . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.0473273 1 160169695 newrs150143470 G T . PASS . GT:GQ:BAF:LRR 0/0:0.402652:0.0114940404892:0.105376 1 160850944 newrs148939374 C A . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:0.0947338 +1 161141636 1KG_1_161141636 G GGCAGTA . PASS . GT:GQ:BAF:LRR 0/0:0.38043:0.0:-0.0657537 +1 161205730 1KG_1_161205730 A AGG . PASS . GT:GQ:BAF:LRR 0/0:0.507577:0.0:0.061392 1 161475798 newrs148134119 G T . PASS . GT:GQ:BAF:LRR 0/0:0.49429:0.0106179714203:-0.0252612 1 165664632 newrs146792904 G A . PASS . GT:GQ:BAF:LRR 0/0:0.496135:0.0:0.0620832 +1 166888531 newrs150392323 TTG T . PASS . GT:GQ:BAF:LRR 0/0:0.893155:0.0:0.0824242 +1 166960707 1KG_1_166960707 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.471949:0.0:0.112189 1 167042622 newrs148369513 C T . PASS . GT:GQ:BAF:LRR 0/0:0.453531:0.0:-0.0277512 +1 167097500 1KG_1_167097500 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.481302:0.0:-0.417604 +1 168154033 1KG_1_168154033 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.429791:0.0:-0.00911786 1 169256540 newrs146620013 C T . PASS . GT:GQ:BAF:LRR 0/0:0.50859:0.0:0.0997077 +1 169512078 1KG_1_169512078 C CTCT . PASS . GT:GQ:BAF:LRR 0/0:0.483117:0.0:-0.218592 +1 170967308 1KG_1_170967308 T TATA . PASS . GT:GQ:BAF:LRR 0/0:0.51365:0.0:0.0419965 +1 171079942 1KG_1_171079942 A AT . PASS . GT:GQ:BAF:LRR 0/0:0.377574:0.0:0.153294 +1 171083456 1KG_1_171083456 TCC T . PASS . GT:GQ:BAF:LRR 0/0:0.516471:0.0:-0.254719 +1 171115566 1KG_1_171115566 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.271776:0.00517083:-1.71432 +1 171174481 1KG_1_171174481 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.465654:0.0:-0.014466 1 171753321 newrs150322704 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500095:0.000733256340027:-0.118102 +1 172411495 1KG_1_172411495 G GACCAGTCCCTAAAA . PASS . GT:GQ:BAF:LRR 0/0:0.443575:0.0:0.108166 +1 172501716 1KG_1_172501716 A AAC . PASS . GT:GQ:BAF:LRR 0/0:0.386971:0.0:0.0432912 1 173807353 newrs149035108 C T . PASS . GT:GQ:BAF:LRR 0/0:0.513198:0.0:0.0379539 1 175325455 newrs146606650 G A . PASS . GT:GQ:BAF:LRR 0/0:0.361595:0.0:-0.0997824 1 179052127 newrs149563285 G A . PASS . GT:GQ:BAF:LRR 0/0:0.493009:0.0230234861374:0.00378964 1 179307032 newrs148646476 G T . PASS . GT:GQ:BAF:LRR 0/0:0.505716:0.0:0.0549275 1 179354442 newrs149782250 C T . PASS . GT:GQ:BAF:LRR 0/0:0.495637:0.0:-0.22645 1 179363138 newrs148772825 G T . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:-0.045627 +1 179503892 1KG_1_179503892 A AGAG . PASS . GT:GQ:BAF:LRR 0/0:0.481375:0.0:-0.177493 +1 179983136 1KG_1_179983136 T TA . PASS . GT:GQ:BAF:LRR 0/0:0.500052:0.0:-0.176441 +1 183087268 1KG_1_183087268 A ATACAGTGAGAGAAG . PASS . GT:GQ:BAF:LRR 0/0:0.516645:0.0:-0.0964463 1 183194742 newrs149195906 G A . PASS . GT:GQ:BAF:LRR 0/0:0.510512:0.0:-0.650326 +1 183899380 1KG_1_183899380 C CAG . PASS . GT:GQ:BAF:LRR 0/0:0.673327:0.0:0.0783064 1 185833761 newrs149911074 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0011528134346:0.0138784 1 186084057 newrs150673369 C T . PASS . GT:GQ:BAF:LRR 0/0:0.489922:0.0:0.073639 +1 186278960 1KG_1_186278960 G GGACT . PASS . GT:GQ:BAF:LRR 0/0:0.480417:0.0:0.133632 1 186281504 newrs150684195 G A . PASS . GT:GQ:BAF:LRR 0/0:0.518561:0.0:0.167807 1 196227323 newrs148932019 C T . PASS . GT:GQ:BAF:LRR 0/0:0.419087:0.0:0.119276 1 196694379 newrs148165372 G A . PASS . GT:GQ:BAF:LRR 0/0:0.897186:0.0:-0.212459 +1 197073231 1KG_1_197073231 A AT . PASS . GT:GQ:BAF:LRR 0/0:0.409735:0.0:0.018068 1 197073245 newrs148294838 G T . PASS . GT:GQ:BAF:LRR 0/0:0.348161:0.0:0.0820793 +1 197383063 1KG_1_197383063 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.875242:0.00133609771729:-0.0568412 +1 200823982 1KG_1_200823982 T TAAC . PASS . GT:GQ:BAF:LRR 0/0:0.511643:0.0:0.0887151 1 201972364 newrs149489527 G T . PASS . GT:GQ:BAF:LRR 0/0:0.402445:0.0:-0.087078 1 202302658 newrs149154798 G A . PASS . GT:GQ:BAF:LRR 0/0:0.51072:0.0:-0.0265459 1 205053076 newrs148879722 G A . PASS . GT:GQ:BAF:LRR 0/0:0.430531:0.0:-0.019981 +1 207134526 1KG_1_207134526 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.467283:0.0:-0.183988 1 207963618 newrs146803767 C T . PASS . GT:GQ:BAF:LRR 0/0:0.507719:0.0:0.0164705 +1 209879176 1KG_1_209879176 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.446978:0.0:-0.0346707 +1 210024646 1KG_1_210024646 A AGAG . PASS . GT:GQ:BAF:LRR 0/0:0.499096:0.0:-0.0463447 1 210536268 newrs149074859 A C . PASS . GT:GQ:BAF:LRR 0/0:0.420059:0.0:0.0323695 +1 211545666 1KG_1_211545666 C CTTCTACA . PASS . GT:GQ:BAF:LRR 0/0:0.493167:0.00920951366425:-0.135812 1 211842488 newrs146817802 G A . PASS . GT:GQ:BAF:LRR 0/0:0.502779:0.0210029482841:-0.98664 1 212911789 newrs150149847 C T . PASS . GT:GQ:BAF:LRR 0/0:0.518952:0.0:0.0199789 +1 212911853 1KG_1_212911853 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.460441:0.0:0.167063 +1 213415338 1KG_1_213415338 C CAGA . PASS . GT:GQ:BAF:LRR 0/0:0.45051:0.0:0.12419 +1 214814173 1KG_1_214814173 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.517305:0.0:0.0757589 +1 215781437 1KG_1_215781437 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.514397:0.0:0.0144966 1 215814065 newrs146733615 G A . PASS . GT:GQ:BAF:LRR 0/0:0.456784:0.0:0.0486638 +1 216420289 1KG_1_216420289 A ATGCACTGCCCTG . PASS . GT:GQ:BAF:LRR 0/0:0.517068:0.0:0.0152525 +1 216420436 1KG_1_216420436 TC T . PASS . GT:GQ:BAF:LRR 0/0:0.494184:0.000855982303619:0.0531604 1 217671697 newrs148242273 C A . PASS . GT:GQ:BAF:LRR 0/0:0.474365:0.0:0.00974765 +1 218504399 1KG_1_218504399 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.414811:0.0:-0.123689 1 220157548 newrs148272159 C T . PASS . GT:GQ:BAF:LRR 0/0:0.506557:0.0:-0.432919 +1 222794607 1KG_1_222794607 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.423082:0.0:-0.067702 1 223176941 newrs147375741 C A . PASS . GT:GQ:BAF:LRR 0/0:0.420376:0.00432181358337:-0.0499767 +1 225428339 1KG_1_225428339 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.443651:0.0:-1.06454 +1 225458504 1KG_1_225458504 T TCAAA . PASS . GT:GQ:BAF:LRR 0/0:0.499601:0.0:-0.342923 1 230895268 newrs146559174 G A . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:0.0876401 +1 231910440 1KG_1_231910440 A AT . PASS . GT:GQ:BAF:LRR 0/0:0.485154:0.0:-0.227934 +1 234563095 1KG_1_234563095 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.467283:0.0:0.0908156 1 235577747 newrs148321184 G A . PASS . GT:GQ:BAF:LRR ./.:0.0787613:0.2217643857:-0.0767733 1 235647638 newrs146580273 C T . PASS . GT:GQ:BAF:LRR 0/0:0.512115:0.0:0.0819448 +1 235875381 1KG_1_235875381 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.512439:0.0:-0.0259097 +1 236706328 1KG_1_236706328 C CTA . PASS . GT:GQ:BAF:LRR 0/0:0.503018:0.0:0.118764 1 237037078 newrs147387989 T C . PASS . GT:GQ:BAF:LRR 0/0:0.514123:0.0:-0.051399 1 237711862 newrs149514924 G A . PASS . GT:GQ:BAF:LRR 0/0:0.759267:0.0:-0.231418 +1 238053825 1KG_1_238053825 C CCT . PASS . GT:GQ:BAF:LRR 0/0:0.444465:0.0160094499588:-0.175253 +1 241846828 newrs146648760 CTG C . PASS . GT:GQ:BAF:LRR ./.:0.0114281:0.18274:-0.134452 +1 244580979 1KG_1_244580979 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.359605:0.0242643:-0.513104 1 247614403 newrs148864378 G T . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0133163928986:-0.00174375 +1 247835614 1KG_1_247835614 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.430013:0.0:0.0982763 2 272247 newrs148640616 C T . PASS . GT:GQ:BAF:LRR 0/0:0.490533:0.0113739967346:-0.251815 +2 9547656 1KG_2_9547656 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.800866:0.0:-0.0965806 +2 9595886 1KG_2_9595886 G GGT . PASS . GT:GQ:BAF:LRR 0/0:0.17156:0.0:0.676754 +2 10350552 1KG_2_10350552 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.511852:0.0:-0.581087 +2 15555719 1KG_2_15555719 T TTAGCTAAAGTTA . PASS . GT:GQ:BAF:LRR 0/0:0.510586:0.0:-0.373451 +2 19552994 1KG_2_19552994 A AAG . PASS . GT:GQ:BAF:LRR 0/0:0.432312:0.0:-0.0912658 +2 20840863 1KG_2_20840863 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.372906:0.0:0.213432 2 21232203 newrs146538280 G A . PASS . GT:GQ:BAF:LRR 0/0:0.486666:0.0:-0.20968 2 21233706 newrs147863759 G A . PASS . GT:GQ:BAF:LRR 0/0:0.419284:0.00512051582336:0.0625729 2 25013405 newrs150693486 G A . PASS . GT:GQ:BAF:LRR 0/0:0.402255:0.0:0.0949489 2 25022714 newrs147240609 G A . PASS . GT:GQ:BAF:LRR 0/0:0.418876:0.00519400835037:0.100752 2 25179912 newrs150189609 C T . PASS . GT:GQ:BAF:LRR 0/0:0.514077:0.0:-0.119383 2 25190147 newrs147784881 G A . PASS . GT:GQ:BAF:LRR 0/0:0.473966:0.0:0.0965744 +2 25383986 1KG_2_25383986 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.519134:0.0:-0.00910194 +2 26533996 1KG_2_26533996 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.408511:0.0:-0.187756 2 27522267 newrs147280617 A G . PASS . GT:GQ:BAF:LRR 0/0:0.514545:0.0105097:-0.131562 2 27702472 newrs150619589 C T . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0127893686295:0.0691737 2 27726415 newrs149847328 C T . PASS . GT:GQ:BAF:LRR 0/0:0.516143:0.0:-0.139037 +2 27850484 1KG_2_27850484 A ATAGCT . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:-0.0179734 2 27891739 newrs147763001 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:0.0355234 2 28754975 newrs146560841 C T . PASS . GT:GQ:BAF:LRR 0/0:0.512898:0.0:-0.27977 +2 28843470 1KG_2_28843470 T TGGAG . PASS . GT:GQ:BAF:LRR 0/0:0.511852:0.0:-0.115682 2 32477660 newrs148696946 C T . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.0662636 2 33526713 newrs149091174 T G . PASS . GT:GQ:BAF:LRR 0/0:0.51335:0.0:-0.103584 2 33749620 newrs147803655 A G . PASS . GT:GQ:BAF:LRR 0/0:0.822063:0.0:-0.00385946 2 37010481 newrs147643782 A G . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.0660986 +2 37082474 1KG_2_37082474 A AC . PASS . GT:GQ:BAF:LRR ./.:0.0110798:0.246029:-0.970781 2 37264998 newrs148649473 A G . PASS . GT:GQ:BAF:LRR 0/0:0.48068:0.0:-0.879975 +2 37265127 1KG_2_37265127 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.510821:0.0:0.0449524 +2 37292978 1KG_2_37292978 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.387575:0.103094:-0.779701 2 37406712 newrs147099571 G A . PASS . GT:GQ:BAF:LRR 0/0:0.496967:0.0:-0.183926 +2 37414552 1KG_2_37414552 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.505147:0.0288379192352:-0.0583204 +2 37475314 1KG_2_37475314 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.868777:0.0:-0.00560107 +2 37483854 1KG_2_37483854 A AT . PASS . GT:GQ:BAF:LRR 0/0:0.411282:0.00700378417969:-0.218663 +2 39262640 1KG_2_39262640 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.500197:0.0:-0.250851 2 39509654 newrs150038225 A G . PASS . GT:GQ:BAF:LRR 0/0:0.499933:0.0:0.00634611 +2 43655276 1KG_2_43655276 C CAGA . PASS . GT:GQ:BAF:LRR 0/0:0.461766:0.0:0.00666627 2 44010657 newrs148986857 A C . PASS . GT:GQ:BAF:LRR 0/0:0.498598:0.0:-0.354151 +2 44209401 1KG_2_44209401 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.493136:0.0:-0.432335 2 44993596 newrs148200193 C T . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:-0.27766 2 45620111 newrs148978058 G A . PASS . GT:GQ:BAF:LRR 0/0:0.456094:0.0:0.0208677 2 45807089 newrs149253392 C A . PASS . GT:GQ:BAF:LRR 0/0:0.498831:0.0:-0.242171 +2 46583886 1KG_2_46583886 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.00138088 2 47637347 newrs149511545 G A . PASS . GT:GQ:BAF:LRR 0/0:0.511852:0.0:0.00770109 2 48686892 newrs146977827 G A . PASS . GT:GQ:BAF:LRR 0/0:0.510909:0.00953328609467:-0.227503 +2 48809230 1KG_2_48809230 T TTTTCATAAGTG . PASS . GT:GQ:BAF:LRR 0/0:0.518427:0.0:0.206784 2 48950760 newrs150650490 C T . PASS . GT:GQ:BAF:LRR 0/0:0.511852:0.00571292638779:0.00218081 2 54081194 newrs148952285 G A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:-0.0998538 +2 54093344 1KG_2_54093344 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.497158:0.0:-0.0900231 2 61411935 newrs148994739 G A . PASS . GT:GQ:BAF:LRR 0/0:0.517442:0.0:-0.0867382 +2 61505301 1KG_2_61505301 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.467283:0.0:-0.107258 +2 62066591 1KG_2_62066591 G GGGCACGGGAGGGT . PASS . GT:GQ:BAF:LRR 0/0:0.452281:0.0:-0.45687 2 63058153 newrs150648830 G A . PASS . GT:GQ:BAF:LRR 0/0:0.511325:0.0:0.0589336 +2 64189230 1KG_2_64189230 C CG . PASS . GT:GQ:BAF:LRR 0/0:0.488259:0.0:0.0808709 2 69297862 newrs148248879 T C . PASS . GT:GQ:BAF:LRR 0/0:0.484905:0.0143264:-0.727175 +2 70502643 1KG_2_70502643 C CAG . PASS . GT:GQ:BAF:LRR 0/0:0.494261:0.0:-0.0855381 +2 71337211 1KG_2_71337211 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.498706:0.0:-0.166835 2 71351536 newrs147401037 T G . PASS . GT:GQ:BAF:LRR 0/0:0.511852:0.0:-0.334952 +2 72362279 1KG_2_72362279 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.488021:0.00354540348053:-0.0747938 +2 73497956 1KG_2_73497956 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.406828:0.0:0.0574934 2 73635852 newrs150825781 C T . PASS . GT:GQ:BAF:LRR 0/0:0.86255:0.0:-0.0263483 2 74450060 newrs148722557 G T . PASS . GT:GQ:BAF:LRR 0/0:0.409735:0.0:0.0999527 2 74750267 newrs150420269 G A . PASS . GT:GQ:BAF:LRR 0/0:0.51373:0.0:-0.148445 2 79254997 newrs147143164 G A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:-0.00317882 +2 84924864 1KG_2_84924864 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.24043:0.0740922:-0.112557 +2 85868121 1KG_2_85868121 A ACT . PASS . GT:GQ:BAF:LRR 0/0:0.517951:0.0:-0.315901 +2 86434383 1KG_2_86434383 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.511678:0.0:0.16192 2 86677062 newrs150111816 C T . PASS . GT:GQ:BAF:LRR 0/0:0.516018:0.0:-0.306152 +2 95815034 1KG_2_95815034 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.50357:0.00915050506592:-0.708913 +2 96992792 1KG_2_96992792 T TGAG . PASS . GT:GQ:BAF:LRR 0/0:0.325996:0.0:0.153105 +2 98418372 1KG_2_98418372 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.50051:0.0:-0.83605 +2 98736048 1KG_2_98736048 C CG . PASS . GT:GQ:BAF:LRR 0/0:0.485555:0.0:-0.103721 2 98986540 newrs147118493 G A . PASS . GT:GQ:BAF:LRR 0/0:0.399199:0.000653743743896:0.0994308 2 99012315 newrs147415641 G A . PASS . GT:GQ:BAF:LRR 0/0:0.491018:0.0:-0.034182 2 99634774 newrs146845080 G T . PASS . GT:GQ:BAF:LRR 0/0:0.364964:0.0:-0.130241 2 103335503 newrs150229633 C T . PASS . GT:GQ:BAF:LRR 0/0:0.457166:0.0:-0.47163 +2 106774541 1KG_2_106774541 T TA . PASS . GT:GQ:BAF:LRR 0/0:0.509648:0.0:-0.180019 +2 112686859 1KG_2_112686859 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.491317:0.00223410129547:0.101156 2 113330180 newrs148462768 C T . PASS . GT:GQ:BAF:LRR 0/0:0.49091:0.0:-0.0910289 +2 122485884 1KG_2_122485884 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.50101:0.0:0.0679682 2 135745136 newrs147939837 C A . PASS . GT:GQ:BAF:LRR 0/0:0.507462:0.0:0.162704 +2 135891505 1KG_2_135891505 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.497747:0.0:0.102511 2 136558283 newrs146614143 C T . PASS . GT:GQ:BAF:LRR 0/0:0.511644:0.0:0.0188863 +2 136594189 1KG_2_136594189 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.42508:0.0:0.00548578 2 141259256 newrs149427515 C A . PASS . GT:GQ:BAF:LRR 0/0:0.510475:0.0:0.212941 +2 152107965 1KG_2_152107965 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.491955:0.0:-0.161658 +2 152320712 1KG_2_152320712 A AAAG . PASS . GT:GQ:BAF:LRR 0/0:0.511418:0.0:0.0175814 2 153415337 newrs148249353 C T . PASS . GT:GQ:BAF:LRR 0/0:0.49181:0.0118697881699:-0.238699 +2 153497308 1KG_2_153497308 C CCTT . PASS . GT:GQ:BAF:LRR 0/0:0.417784:0.0:-0.0326498 +2 158971739 1KG_2_158971739 A ATG . PASS . GT:GQ:BAF:LRR 0/0:0.455833:0.0:-0.0924625 2 158977989 newrs148797309 C T . PASS . GT:GQ:BAF:LRR 0/0:0.510234:0.0051736831665:-0.432319 +2 160628451 1KG_2_160628451 C CTG . PASS . GT:GQ:BAF:LRR 0/0:0.471466:0.0:-0.387083 2 160697239 newrs149752222 C T . PASS . GT:GQ:BAF:LRR 0/0:0.495101:0.00832676887512:0.0413836 2 160826719 newrs146991124 G T . PASS . GT:GQ:BAF:LRR 0/0:0.495752:0.0:0.141565 2 170387132 newrs148187838 G A . PASS . GT:GQ:BAF:LRR 0/0:0.498764:0.0:-0.714172 2 171715408 newrs147201199 G A . PASS . GT:GQ:BAF:LRR 0/0:0.499822:0.0:-0.461191 +2 171812947 1KG_2_171812947 T TCC . PASS . GT:GQ:BAF:LRR 0/0:0.378449:0.0:-0.123853 +2 172928566 1KG_2_172928566 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.403676:0.0:0.0109238 2 173352274 newrs148112672 G A . PASS . GT:GQ:BAF:LRR 0/0:0.485714:0.0:-0.00548074 +2 173662291 1KG_2_173662291 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.473604:0.00167936086655:-0.101517 2 174231932 newrs150220964 C T . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:0.080326 +2 178565852 1KG_2_178565852 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.423495:0.0612238:-1.05278 +2 178681632 1KG_2_178681632 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.500075:0.0172103643417:0.0604811 +2 179505311 1KG_2_179505311 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.500144:0.0:0.123037 2 179602841 newrs147879266 C T . PASS . GT:GQ:BAF:LRR 0/0:0.889129:0.0:-0.184389 2 179632509 newrs146572907 G A . PASS . GT:GQ:BAF:LRR 0/0:0.518824:0.0:0.0425156 2 182468660 newrs147234433 C A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.00178442 +2 182543454 1KG_2_182543454 G GTTTCGAGGTCGTCCTC . PASS . GT:GQ:BAF:LRR 0/0:0.433696:0.0:-0.150443 +2 183011859 1KG_2_183011859 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.499626:0.0:-0.739007 +2 183595804 1KG_2_183595804 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.429791:0.0:0.196131 +2 183621108 1KG_2_183621108 AAC A . PASS . GT:GQ:BAF:LRR 0/0:0.513273:0.0:0.0288578 2 187626443 newrs149426133 C T . PASS . GT:GQ:BAF:LRR 0/0:0.517635:0.0:-0.160677 2 189861949 newrs146652498 G A . PASS . GT:GQ:BAF:LRR 0/0:0.894299:0.0:0.0337128 2 189872776 newrs147706051 A G . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.133614 2 189948710 newrs150092345 C T . PASS . GT:GQ:BAF:LRR 0/0:0.312364:0.0138638019562:0.0751853 +2 190331308 1KG_2_190331308 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.51361:0.0:0.0567394 +2 190531850 1KG_2_190531850 A AT . PASS . GT:GQ:BAF:LRR 0/0:0.496314:0.0:-0.013749 2 190728842 newrs148214055 G T . PASS . GT:GQ:BAF:LRR 0/0:0.503287:0.0:-0.0496794 +2 191940963 1KG_2_191940963 A AT . PASS . GT:GQ:BAF:LRR 0/0:0.488085:0.0:0.0729098 2 197143252 newrs148753553 C T . PASS . GT:GQ:BAF:LRR 0/0:0.430166:0.00457906723022:-0.373217 +2 197531518 1KG_2_197531518 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.380991:0.0:0.0226204 +2 197645349 1KG_2_197645349 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.511852:0.00307250022888:-0.0552804 +2 197649613 1KG_2_197649613 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.49687:0.0:-0.571154 2 198011817 newrs147529433 G A . PASS . GT:GQ:BAF:LRR 0/0:0.511407:0.0:0.102923 +2 198571431 1KG_2_198571431 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:-0.0617951 +2 200246515 1KG_2_200246515 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.500156:0.00442466:-0.590698 2 201468080 newrs148871699 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.0827931 2 201485454 newrs148848561 G T . PASS . GT:GQ:BAF:LRR 0/0:0.514503:0.0:-0.0231242 2 201746205 newrs148778524 C T . PASS . GT:GQ:BAF:LRR 0/0:0.458434:0.0:-0.254425 2 202139656 newrs146816437 G T . PASS . GT:GQ:BAF:LRR 0/0:0.480718:0.0:-0.98259 +2 205912378 1KG_2_205912378 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.00534152984619:-0.0195225 +2 207631459 1KG_2_207631459 G GAGCAAAATGAAT . PASS . GT:GQ:BAF:LRR 0/0:0.514304:0.0:-0.0394533 +2 211060027 1KG_2_211060027 A ATG . PASS . GT:GQ:BAF:LRR 0/0:0.523617:0.0:-0.0692448 +2 211085410 1KG_2_211085410 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.486853:0.0:0.324943 2 211481201 newrs147062907 A G . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.0480907 2 213872794 newrs146574423 G A . PASS . GT:GQ:BAF:LRR 0/0:0.516934:0.0:0.0531858 2 214161989 newrs147302970 C A . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.00729429721832:0.13887 +2 214727221 1KG_2_214727221 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.374745:0.0:0.103157 2 215595159 newrs147215925 T C . PASS . GT:GQ:BAF:LRR 0/0:0.799495:0.0:-0.0562691 +2 215645502 1KG_2_215645502 G GTGGTGAAGAACATTCAGGCAA . PASS . GT:GQ:BAF:LRR 0/0:0.437144:0.0:0.0472644 +2 215852499 1KG_2_215852499 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.362255:0.0:-0.431405 2 219141726 newrs150313254 C T . PASS . GT:GQ:BAF:LRR 0/0:0.508287:0.0:0.10109 +2 219616476 1KG_2_219616476 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.376071:0.0:-0.0899592 2 220045436 newrs150059479 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.124957 +2 220085566 1KG_2_220085566 A AGAGGCAGCC . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0188492:0.00890678 +2 220101968 1KG_2_220101968 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.000237012:-0.0447065 +2 220147886 1KG_2_220147886 T TGG . PASS . GT:GQ:BAF:LRR 0/0:0.42453:0.0:0.139665 2 220285366 newrs146755676 G A . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:-0.00476619 2 224463265 newrs149795847 C T . PASS . GT:GQ:BAF:LRR 0/0:0.371617:0.0:0.0363237 2 224831713 newrs149165411 G T . PASS . GT:GQ:BAF:LRR 0/0:0.508769:0.0:-0.091282 +2 225717795 1KG_2_225717795 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.412666:0.0:0.012215 +2 227731951 1KG_2_227731951 C CG . PASS . GT:GQ:BAF:LRR 0/0:0.498303:0.00615001:-1.1371 +2 230650565 1KG_2_230650565 C CAGTA . PASS . GT:GQ:BAF:LRR 0/0:0.483652:0.0:-0.049045 2 233625195 newrs149250246 G T . PASS . GT:GQ:BAF:LRR 0/0:0.388034:0.0:0.0264922 +2 233744309 1KG_2_233744309 T TGG . PASS . GT:GQ:BAF:LRR 0/0:0.462962:0.0:-0.0137276 2 234590826 newrs149618508 C A . PASS . GT:GQ:BAF:LRR 0/0:0.280187:0.012552022934:0.132973 +2 237076578 1KG_2_237076578 G GCAT . PASS . GT:GQ:BAF:LRR 0/0:0.508784:0.0:0.153331 +2 242432411 1KG_2_242432411 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.330772:0.0847543:-0.863124 +3 8672567 1KG_3_8672567 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.426687:0.0:-0.197509 +3 8675613 1KG_3_8675613 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.483202:0.0:-0.152506 +3 9412793 1KG_3_9412793 C CAA . PASS . GT:GQ:BAF:LRR 0/0:0.497073:0.00191974639893:-0.504537 3 9426235 newrs149283084 C T . PASS . GT:GQ:BAF:LRR 0/0:0.481868:0.00136929750443:0.157917 +3 9974362 1KG_3_9974362 C CCTT . PASS . GT:GQ:BAF:LRR 0/0:0.518295:0.0:0.135903 +3 9976537 1KG_3_9976537 C CG . PASS . GT:GQ:BAF:LRR 0/0:0.480417:0.0:-0.262304 3 10136006 newrs148471911 C T . PASS . GT:GQ:BAF:LRR 0/0:0.487384:0.0247240066528:-0.0304888 +3 10251374 1KG_3_10251374 A AAG . PASS . GT:GQ:BAF:LRR 0/0:0.519042:0.0:0.153887 3 10953879 newrs149375519 G A . PASS . GT:GQ:BAF:LRR 0/0:0.516017:0.0:0.0202665 +3 10980068 1KG_3_10980068 G GAGA . PASS . GT:GQ:BAF:LRR 0/0:0.440661:0.0:-0.0474124 +3 12195046 1KG_3_12195046 C CTGA . PASS . GT:GQ:BAF:LRR 0/0:0.420112:0.0:0.0348874 +3 12198913 1KG_3_12198913 A AT . PASS . GT:GQ:BAF:LRR 0/0:0.49371:0.0:-1.37244 +3 12421304 1KG_3_12421304 A AT . PASS . GT:GQ:BAF:LRR 0/0:0.424847:0.017582654953:0.113203 3 12560697 newrs149417061 G A . PASS . GT:GQ:BAF:LRR 0/0:0.512616:0.00385147333145:0.0207241 +3 12571369 1KG_3_12571369 T TA . PASS . GT:GQ:BAF:LRR 0/0:0.501382:0.0:0.0697926 3 12791254 newrs149474579 C T . PASS . GT:GQ:BAF:LRR 0/0:0.509778:0.0:0.0885353 +3 13417857 1KG_3_13417857 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.389878:0.0:0.221126 +3 13663291 1KG_3_13663291 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.00143718719482:0.010721 3 14174410 newrs147336367 C T . PASS . GT:GQ:BAF:LRR 0/0:0.435188:0.0:-0.173993 3 14745899 newrs146642906 C T . PASS . GT:GQ:BAF:LRR 0/0:0.711028:0.020172894001:-0.126525 3 15288911 newrs149691332 C A . PASS . GT:GQ:BAF:LRR 0/0:0.373656:0.0624018907547:-0.281421 3 15686732 newrs146600671 G A . PASS . GT:GQ:BAF:LRR 0/0:0.497704:0.0:-0.166274 +3 16343174 1KG_3_16343174 G GTTC . PASS . GT:GQ:BAF:LRR 0/0:0.498983:0.0:-0.296169 +3 20043188 1KG_3_20043188 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.505952:0.000331521034241:-0.148036 3 21706378 newrs147583836 C T . PASS . GT:GQ:BAF:LRR 0/0:0.529052:0.0:-0.0763009 3 32801063 newrs146801343 A C . PASS . GT:GQ:BAF:LRR 0/0:0.528879:0.0:0.152315 3 37150133 newrs149602102 G A . PASS . GT:GQ:BAF:LRR 0/0:0.506383:0.0112701654434:-0.0832593 +3 37459158 1KG_3_37459158 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.814377:0.0:-0.80517 +3 37459158 newrs149414048 GA G . PASS . GT:GQ:BAF:LRR 0/0:0.837869:0.0308653:-1.61992 3 38053166 newrs148984703 T G . PASS . GT:GQ:BAF:LRR 0/0:0.483202:0.0:0.0454614 3 38061820 newrs148796522 G A . PASS . GT:GQ:BAF:LRR 0/0:0.468348:0.0424809455872:-0.235997 3 38307727 newrs147778100 G T . PASS . GT:GQ:BAF:LRR 0/0:0.513792:0.000425398349762:0.14366 @@ -247,50 +453,81 @@ 3 38966906 newrs146942592 G A . PASS . GT:GQ:BAF:LRR 0/0:0.513848:0.0:-0.110957 3 39178003 newrs148431487 G T . PASS . GT:GQ:BAF:LRR 0/0:0.512985:0.0:0.0317934 3 40353062 newrs147698288 G A . PASS . GT:GQ:BAF:LRR 0/0:0.502759:0.0:0.00390594 +3 42264448 1KG_3_42264448 C CAACTCCAGCTTGTGGCAGCA . PASS . GT:GQ:BAF:LRR 0/0:0.399126:0.0595827102661:-0.248549 3 42955929 newrs147863526 G T . PASS . GT:GQ:BAF:LRR 0/0:0.515244:0.00456595420837:0.0228084 +3 44286168 1KG_3_44286168 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.343703:0.00744122:0.190014 3 44701410 newrs148645131 C T . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:0.0124902 3 44762610 newrs146541622 G T . PASS . GT:GQ:BAF:LRR 0/0:0.512367:2.14576721191e-06:0.0573141 3 44932143 newrs148772351 C T . PASS . GT:GQ:BAF:LRR 0/0:0.462291:0.0:0.135343 3 46415393 newrs147879075 C T . PASS . GT:GQ:BAF:LRR 0/0:0.49784:0.0107857584953:-0.689954 3 46479574 newrs150670421 A C . PASS . GT:GQ:BAF:LRR 0/0:0.374745:0.0:0.0508686 +3 46786201 1KG_3_46786201 A ATT . PASS . GT:GQ:BAF:LRR 0/0:0.475078:0.0137226581573:-0.605786 +3 47084126 1KG_3_47084126 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.411598 3 48215773 newrs149350315 C A . PASS . GT:GQ:BAF:LRR 0/0:0.51022:0.0:0.160297 +3 49149418 1KG_3_49149418 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.400863:0.0:0.126095 3 49318198 newrs150287339 C A . PASS . GT:GQ:BAF:LRR 0/0:0.399452:0.0:0.172546 +3 50332887 1KG_3_50332887 G GTGCACACCAAAGC . PASS . GT:GQ:BAF:LRR 0/0:0.438779:0.0:0.0101531 +3 51937032 1KG_3_51937032 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.376958:0.0:0.193523 +3 52380742 1KG_3_52380742 C CGG . PASS . GT:GQ:BAF:LRR 0/0:0.461561:0.0:0.0828765 3 52786032 newrs146877089 C T . PASS . GT:GQ:BAF:LRR 0/0:0.49897:0.0137360095978:-0.468127 3 53886024 newrs149538576 A C . PASS . GT:GQ:BAF:LRR 0/0:0.289345:0.0:0.0668447 3 56601067 newrs149475199 G A . PASS . GT:GQ:BAF:LRR 0/0:0.487683:0.0:0.039046 +3 56653813 1KG_3_56653813 CA C . PASS . GT:GQ:BAF:LRR 0/0:0.449554:0.0266268:-0.863093 +3 56655621 1KG_3_56655621 A AAGAG . PASS . GT:GQ:BAF:LRR 0/0:0.4939:0.0:-0.0627347 3 58494643 newrs147680655 G A . PASS . GT:GQ:BAF:LRR 0/0:0.499881:0.0:0.0510018 3 58519760 newrs149540578 G A . PASS . GT:GQ:BAF:LRR 0/0:0.376958:0.0:0.0841575 +3 63981592 1KG_3_63981592 T TA . PASS . GT:GQ:BAF:LRR ./.:0.0129809:0.123751819134:-0.0342205 +3 65372849 1KG_3_65372849 T TTC . PASS . GT:GQ:BAF:LRR 0/0:0.337342:0.0:0.0972976 3 69988298 newrs149249176 G A . PASS . GT:GQ:BAF:LRR 0/0:0.49553:0.0:0.0267149 3 71748775 newrs149437626 G A . PASS . GT:GQ:BAF:LRR 0/0:0.513289:0.0:-0.23323 3 73657837 newrs149396248 T G . PASS . GT:GQ:BAF:LRR 0/0:0.48671:0.0:-0.0723483 +3 88040567 1KG_3_88040567 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:0.164914 +3 88199240 1KG_3_88199240 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.429791:0.0:-0.762652 +3 97806298 newrs146746951 AT A . PASS . GT:GQ:BAF:LRR 0/0:0.786032:0.0:0.101395 +3 101476554 1KG_3_101476554 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.3786:0.0503166:-0.167136 +3 105470388 1KG_3_105470388 A AT . PASS . GT:GQ:BAF:LRR 0/0:0.480624:0.0:0.149448 3 107497349 newrs150437555 C T . PASS . GT:GQ:BAF:LRR 0/0:0.459837:0.0:0.0404126 3 107510124 newrs149104597 G A . PASS . GT:GQ:BAF:LRR 0/0:0.500553:0.0:-0.299453 +3 108074128 1KG_3_108074128 T TAACA . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:0.0422716 +3 108112986 1KG_3_108112986 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.326773:0.0:-0.811615 3 109027122 newrs150350350 G A . PASS . GT:GQ:BAF:LRR 0/0:0.413243:0.00371915102005:-0.0767541 3 109052769 newrs150133131 T C . PASS . GT:GQ:BAF:LRR 0/0:0.420089:0.0:-0.0862267 3 111343251 newrs150804090 T C . PASS . GT:GQ:BAF:LRR 0/0:0.511852:0.0:-0.117912 3 111799851 newrs147783135 C T . PASS . GT:GQ:BAF:LRR 0/0:0.487442:0.0:-0.37333 +3 111918232 1KG_3_111918232 T TCTG . PASS . GT:GQ:BAF:LRR 0/0:0.483202:0.0:0.139616 3 113286557 newrs148646920 G A . PASS . GT:GQ:BAF:LRR 0/0:0.500101:0.0:0.00803275 3 113335009 newrs150137878 C T . PASS . GT:GQ:BAF:LRR 0/0:0.478579:0.0:-0.0937002 +3 113499971 1KG_3_113499971 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.511852:0.0104419589043:0.0733389 +3 113955808 1KG_3_113955808 A ACTTGGTC . PASS . GT:GQ:BAF:LRR 0/0:0.397703:0.0:-0.0296122 3 119211127 newrs150029976 A C . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.0675809 3 119325752 newrs148143400 G T . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.0125678 3 119434591 newrs147597066 G A . PASS . GT:GQ:BAF:LRR 0/0:0.512854:0.0:0.139649 3 121202346 newrs150312701 G A . PASS . GT:GQ:BAF:LRR 0/0:0.503841:0.00116169452667:-0.197379 3 121345582 newrs149561440 G A . PASS . GT:GQ:BAF:LRR 0/0:0.374745:0.0255137085915:0.018823 +3 121516039 1KG_3_121516039 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.487384:0.0:0.0415161 3 121658264 newrs148008499 G A . PASS . GT:GQ:BAF:LRR 0/0:0.495217:0.0:-0.157029 +3 122459289 1KG_3_122459289 T TGA . PASS . GT:GQ:BAF:LRR 0/0:0.862101:0.0:-0.338648 3 122487730 newrs150320476 C A . PASS . GT:GQ:BAF:LRR 0/0:0.508439:0.0:-0.154177 +3 122525716 1KG_3_122525716 C CTG . PASS . GT:GQ:BAF:LRR 0/0:0.506335:0.0:-0.46494 +3 122978424 1KG_3_122978424 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.479976:0.0:0.0135069 +3 124854612 1KG_3_124854612 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:-0.0547705 3 125188298 newrs150435491 A G . PASS . GT:GQ:BAF:LRR 0/0:0.500145:0.0:-0.0860629 3 128612406 newrs148694290 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500042:0.0:-0.718188 3 130282510 newrs150427289 T C . PASS . GT:GQ:BAF:LRR 0/0:0.828074:0.0:-0.136943 3 130871352 newrs150253539 T G . PASS . GT:GQ:BAF:LRR 0/0:0.438791:0.0:0.329487 3 132036382 newrs149109145 C T . PASS . GT:GQ:BAF:LRR 0/0:0.517813:0.0:-0.211665 +3 132278688 1KG_3_132278688 A AGG . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.448264 3 132400757 newrs147332157 C T . PASS . GT:GQ:BAF:LRR 0/0:0.516853:0.0:0.0418239 3 132407950 newrs148670389 G A . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:0.120365 3 133473346 newrs150548621 G A . PASS . GT:GQ:BAF:LRR 0/0:0.51048:0.0:-0.0776137 3 133553479 newrs147187493 G A . PASS . GT:GQ:BAF:LRR 0/0:0.497686:0.0:-0.650794 +3 134269034 1KG_3_134269034 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.49444:0.0:-0.0757921 +3 137822323 1KG_3_137822323 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.494267:0.0:0.0515331 3 137886048 newrs149610079 G A . PASS . GT:GQ:BAF:LRR 0/0:0.514725:0.0:-0.192194 3 138248217 newrs146572731 C T . PASS . GT:GQ:BAF:LRR 0/0:0.499361:0.0:0.165248 3 141626116 newrs149224279 C T . PASS . GT:GQ:BAF:LRR 0/0:0.517493:0.0:0.0157167 3 142408660 newrs148218811 G A . PASS . GT:GQ:BAF:LRR 0/0:0.322583:0.0:-0.0247877 +3 146309608 1KG_3_146309608 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.454777:0.0:-0.569752 3 148459591 newrs150330554 C T . PASS . GT:GQ:BAF:LRR 0/0:0.387978:0.0:-0.0471387 3 148759953 newrs149074331 C T . PASS . GT:GQ:BAF:LRR 0/0:0.458472:0.0:0.129733 3 150931294 newrs148423792 C A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.081865 @@ -298,23 +535,34 @@ 3 154802023 newrs150836510 C T . PASS . GT:GQ:BAF:LRR 0/0:0.507578:0.0:-0.565702 3 154862172 newrs149905705 C T . PASS . GT:GQ:BAF:LRR 0/0:0.514676:0.0:-0.290743 3 160156268 newrs150089676 A C . PASS . GT:GQ:BAF:LRR 0/0:0.498265:0.0:0.0487368 +3 160156756 1KG_3_160156756 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.513674:0.0:-0.266051 +3 165547489 1KG_3_165547489 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.487179:0.00740103:-0.770525 3 165548629 newrs148170012 G A . PASS . GT:GQ:BAF:LRR 0/0:0.501483:0.0:-0.219884 3 167159974 newrs148696355 C T . PASS . GT:GQ:BAF:LRR 0/0:0.503189:0.0:0.0689014 3 167189391 newrs150619093 G A . PASS . GT:GQ:BAF:LRR 0/0:0.481547:0.0:0.0828095 +3 167759246 1KG_3_167759246 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.487239:0.0108273029327:-0.0606661 3 169511489 newrs146621484 A C . PASS . GT:GQ:BAF:LRR 0/0:0.483108:0.0:0.138287 3 172482204 newrs148663230 G A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.121419 3 172634118 newrs146640459 C A . PASS . GT:GQ:BAF:LRR 0/0:0.511852:0.0:0.173031 3 172674467 newrs149140561 C T . PASS . GT:GQ:BAF:LRR 0/0:0.484945:0.00206476449966:0.14995 +3 180334625 1KG_3_180334625 C CTCTT . PASS . GT:GQ:BAF:LRR 0/0:0.51604:0.0:0.0483164 +3 180379692 1KG_3_180379692 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.429791:0.00784146:0.344642 +3 182616397 1KG_3_182616397 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.49957:0.0:0.128241 3 183211920 newrs147068041 G A . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:0.00196975 +3 184910917 1KG_3_184910917 A ATC . PASS . GT:GQ:BAF:LRR 0/0:0.389878:0.0:0.0385994 3 184922543 newrs146633671 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.0319869 3 185879392 newrs149298788 C T . PASS . GT:GQ:BAF:LRR 0/0:0.437916:0.0:-0.0617891 +3 186274538 1KG_3_186274538 A AGC . PASS . GT:GQ:BAF:LRR 0/0:0.434559:0.0:-0.167463 3 186289915 newrs148976481 C T . PASS . GT:GQ:BAF:LRR 0/0:0.465095:0.0:-0.0633064 3 186510326 newrs150799698 G A . PASS . GT:GQ:BAF:LRR 0/0:0.511468:0.0:-0.137579 3 186510593 newrs147162624 C T . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.175528 3 186940950 newrs148556944 G A . PASS . GT:GQ:BAF:LRR 0/0:0.443245:0.00648820400238:0.038031 +3 189028287 1KG_3_189028287 C CCT . PASS . GT:GQ:BAF:LRR 0/0:0.527049:0.0:0.0936655 3 192973578 newrs149064282 G A . PASS . GT:GQ:BAF:LRR 0/0:0.505164:0.0127172470093:-0.531173 3 193036880 newrs148097145 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.131214 +3 193332586 1KG_3_193332586 T TTTCACGAAGCATTTATCA . PASS . GT:GQ:BAF:LRR 0/0:0.490141:0.0:-0.120217 3 193365922 newrs147077380 G A . PASS . GT:GQ:BAF:LRR 0/0:0.475612:0.0:0.0377081 +3 194180610 1KG_3_194180610 G GCTT . PASS . GT:GQ:BAF:LRR 0/0:0.515334:0.0:-0.101439 3 194313800 newrs150713705 C T . PASS . GT:GQ:BAF:LRR 0/0:0.499083:0.00878554582596:0.105485 3 195785154 newrs147330019 C T . PASS . GT:GQ:BAF:LRR 0/0:0.478774:0.0:0.00708426 3 196214335 newrs148275050 G A . PASS . GT:GQ:BAF:LRR 0/0:0.39725:0.0:-0.154492 @@ -322,97 +570,188 @@ 4 366855 newrs147483014 G A . PASS . GT:GQ:BAF:LRR 0/0:0.263285:0.0:0.00338186 4 844776 newrs149731617 G A . PASS . GT:GQ:BAF:LRR 0/0:0.509334:0.0:0.105907 4 890248 newrs149963126 C T . PASS . GT:GQ:BAF:LRR 0/0:0.497629:0.0:-0.0712523 +4 2240569 1KG_4_2240569 C CTT . PASS . GT:GQ:BAF:LRR 0/0:0.492341:0.0:0.142333 +4 2514182 1KG_4_2514182 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.411715:0.0:0.0996149 4 2948210 newrs150411289 G A . PASS . GT:GQ:BAF:LRR 0/0:0.354281:0.0459765195847:-0.329292 +4 4242109 1KG_4_4242109 C CAT . PASS . GT:GQ:BAF:LRR 0/0:0.510081:0.0:0.227235 4 4322933 newrs148926395 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:0.141315 4 8383293 newrs146945288 G A . PASS . GT:GQ:BAF:LRR 0/0:0.502229:0.0:-0.102048 4 8467193 newrs147229355 C T . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.0884682 +4 26407846 1KG_4_26407846 A AT . PASS . GT:GQ:BAF:LRR 0/0:0.473321:0.0441386699677:-0.633335 +4 26491098 1KG_4_26491098 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.351573:0.0:-0.578326 4 36345134 newrs149895631 G A . PASS . GT:GQ:BAF:LRR 0/0:0.758343:0.0:-0.0648703 +4 39088347 1KG_4_39088347 G GGTAA . PASS . GT:GQ:BAF:LRR 0/0:0.528749:0.00849868:0.0138503 4 40144398 newrs149506250 C T . PASS . GT:GQ:BAF:LRR 0/0:0.471953:0.0:0.0939122 4 48037577 newrs148207193 A G . PASS . GT:GQ:BAF:LRR 0/0:0.509715:0.0:-0.036752 4 48852065 newrs148329796 C T . PASS . GT:GQ:BAF:LRR 0/0:0.499734:0.0:-0.228192 4 48993509 newrs149499062 C T . PASS . GT:GQ:BAF:LRR 0/0:0.502054:0.0:-0.100949 +4 52861333 1KG_4_52861333 C CCA . PASS . GT:GQ:BAF:LRR 0/0:0.410435:0.0:-0.046154 +4 52861667 1KG_4_52861667 GGAATA G . PASS . GT:GQ:BAF:LRR 0/0:0.361595:0.0:0.049437 4 52895932 newrs150518260 G A . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:0.153992 +4 55976832 1KG_4_55976832 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.370676:0.0:-0.599928 4 57215500 newrs149271822 C T . PASS . GT:GQ:BAF:LRR 0/0:0.473282:0.0:-0.0322665 +4 62599243 1KG_4_62599243 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.42763:0.0:0.0240074 4 68447022 newrs147302126 G A . PASS . GT:GQ:BAF:LRR 0/0:0.422059:0.0:-0.196124 +4 68606363 1KG_4_68606363 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.0836954 4 68606388 newrs148499544 A C . PASS . GT:GQ:BAF:LRR 0/0:0.519131:0.0:-0.137615 4 68938040 newrs148214799 C T . PASS . GT:GQ:BAF:LRR 0/0:0.487435:0.0:0.228372 4 69342156 newrs147196017 C T . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.0483638 4 70596214 newrs148007908 T G . PASS . GT:GQ:BAF:LRR 0/0:0.514785:0.0:0.146563 +4 70810660 1KG_4_70810660 C CG . PASS . GT:GQ:BAF:LRR 0/0:0.376958:0.0:0.0807748 4 71507790 newrs146706831 C T . PASS . GT:GQ:BAF:LRR 0/0:0.497783:0.00540226697922:-0.0569451 4 71670135 newrs147166750 T C . PASS . GT:GQ:BAF:LRR 0/0:0.432716:0.0:0.0936925 +4 72635068 1KG_4_72635068 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.492057:0.0:-0.211133 4 73178008 newrs146827790 G A . PASS . GT:GQ:BAF:LRR 0/0:0.322395:0.0:-0.246146 4 73184295 newrs150704470 G T . PASS . GT:GQ:BAF:LRR 0/0:0.498366:0.0:-0.364079 4 74284028 newrs149079814 C T . PASS . GT:GQ:BAF:LRR 0/0:0.501102:0.011549949646:-0.388384 4 74365763 newrs147051358 C T . PASS . GT:GQ:BAF:LRR 0/0:0.344362:0.0:-0.0723751 4 76489574 newrs146645381 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.0526185 +4 81207686 1KG_4_81207686 G GAGC . PASS . GT:GQ:BAF:LRR 0/0:0.742128:0.0:0.136957 4 89671574 newrs148165624 C A . PASS . GT:GQ:BAF:LRR 0/0:0.487661:0.0:-0.128073 4 90844405 newrs146692577 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500204:0.00161904096603:0.199314 4 98865046 newrs150178155 A G . PASS . GT:GQ:BAF:LRR 0/0:0.514402:0.0:-0.0980106 4 100826754 newrs149618769 G A . PASS . GT:GQ:BAF:LRR 0/0:0.233143:0.0699843168259:-0.0372861 +4 103504086 1KG_4_103504086 A AT . PASS . GT:GQ:BAF:LRR 0/0:0.478924:0.0672519207001:-1.28548 +4 103590196 1KG_4_103590196 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.495684:0.0:-0.399698 +4 107092300 1KG_4_107092300 C CG . PASS . GT:GQ:BAF:LRR 0/0:0.401705:0.0:-0.0520617 +4 107252859 1KG_4_107252859 T TAG . PASS . GT:GQ:BAF:LRR 0/0:0.482424:0.0:-0.133141 4 109667672 newrs146606272 G A . PASS . GT:GQ:BAF:LRR 0/0:0.487384:0.0:-0.00448393 4 110617569 newrs148210591 C A . PASS . GT:GQ:BAF:LRR 0/0:0.481828:0.0:0.132258 4 111474579 newrs148232326 G A . PASS . GT:GQ:BAF:LRR 0/0:0.509057:0.00473064184189:0.193807 +4 113352617 1KG_4_113352617 G GCATT . PASS . GT:GQ:BAF:LRR 0/0:0.529569:0.0:-0.0160461 4 114430793 newrs148603207 C T . PASS . GT:GQ:BAF:LRR 0/0:0.510791:0.0:0.0720721 +4 114469824 1KG_4_114469824 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.483202:0.039818:-0.435594 +4 115544168 1KG_4_115544168 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.399738:9.29832458496e-06:0.0109129 4 119239531 newrs149455950 A G . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.0354826 4 122593688 newrs146935113 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.0914721 4 122593712 newrs147110745 G A . PASS . GT:GQ:BAF:LRR 0/0:0.503454:0.0:-0.0155689 4 122682805 newrs148344547 G A . PASS . GT:GQ:BAF:LRR 0/0:0.499527:0.00511652231216:0.0971537 4 123868644 newrs149688478 G A . PASS . GT:GQ:BAF:LRR 0/0:0.504149:0.0:-0.237321 4 126408554 newrs148483308 G T . PASS . GT:GQ:BAF:LRR 0/0:0.497407:0.0:-0.217825 +4 128807333 1KG_4_128807333 T TCAA . PASS . GT:GQ:BAF:LRR 0/0:0.529569:0.0:0.0349729 +4 128807692 1KG_4_128807692 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.361801:0.0100836:0.167114 4 128859937 newrs148601655 C A . PASS . GT:GQ:BAF:LRR 0/0:0.509562:0.0:-0.260451 4 141484263 newrs147778681 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500305:0.0:0.045705 +4 146601514 1KG_4_146601514 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.897003:0.0:-0.127363 4 148800491 newrs150075964 T G . PASS . GT:GQ:BAF:LRR 0/0:0.409735:0.0:-0.199415 +4 151789436 1KG_4_151789436 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.492527:0.0128811597824:-0.189858 +4 152054191 1KG_4_152054191 A AG . PASS . GT:GQ:BAF:LRR 0/1:0.345433:0.391183:-0.832535 +4 156135773 1KG_4_156135773 T TTG . PASS . GT:GQ:BAF:LRR 0/0:0.518913:0.0:-0.00948344 +4 159158784 1KG_4_159158784 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.480032:0.0:-0.0285994 +4 159573028 1KG_4_159573028 T TACAG . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:0.0772208 4 164393674 newrs148025040 G A . PASS . GT:GQ:BAF:LRR 0/0:0.480375:0.0:-0.0182719 4 169085406 newrs147539910 G T . PASS . GT:GQ:BAF:LRR 0/0:0.518436:0.0:0.0309299 4 169183151 newrs148697677 C T . PASS . GT:GQ:BAF:LRR 0/0:0.498627:0.0104211568832:0.0222474 4 169204597 newrs150794038 G A . PASS . GT:GQ:BAF:LRR 0/0:0.500974:0.0:0.252788 +4 169362513 1KG_4_169362513 A AAG . PASS . GT:GQ:BAF:LRR 0/0:0.518425:0.0:-0.590218 4 170190228 newrs150585496 C A . PASS . GT:GQ:BAF:LRR 0/0:0.514203:0.0:0.0413681 +4 177069408 1KG_4_177069408 G GACTAT . PASS . GT:GQ:BAF:LRR 0/0:0.500168:0.0:-0.0236006 +4 177608420 1KG_4_177608420 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.495611:0.0:-0.0035216 4 178354368 newrs149870867 C T . PASS . GT:GQ:BAF:LRR 0/0:0.511559:0.0:0.124945 +4 184431770 1KG_4_184431770 A ATT . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.0:0.114375 4 184585162 newrs150331292 C T . PASS . GT:GQ:BAF:LRR 0/0:0.45756:0.0:0.0838093 4 184605164 newrs150383310 G A . PASS . GT:GQ:BAF:LRR 0/0:0.500987:0.0125321149826:0.0583266 +4 184628077 1KG_4_184628077 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:-0.0167878 +4 184930730 1KG_4_184930730 T TCCTATA . PASS . GT:GQ:BAF:LRR 0/0:0.529569:0.0:0.103787 +4 186111420 1KG_4_186111420 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.037991 +4 186320910 1KG_4_186320910 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.395421:0.0:0.0201995 4 186329171 newrs150505755 G T . PASS . GT:GQ:BAF:LRR 0/0:0.466408:0.000649333000183:0.103331 +4 187004230 1KG_4_187004230 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.517968:0.0:-0.106423 +4 187455067 1KG_4_187455067 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.0452672 +4 187519247 1KG_4_187519247 C CTA . PASS . GT:GQ:BAF:LRR 0/0:0.487258:0.0136796236038:0.124391 +5 256483 1KG_5_256483 C CTT . PASS . GT:GQ:BAF:LRR 0/0:0.517947:0.0:0.0809048 +5 1076292 1KG_5_1076292 C CGTA . PASS . GT:GQ:BAF:LRR 0/0:0.502797:0.0:-0.114157 5 6602573 newrs149980835 C T . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.117721 5 7867002 newrs148214151 G A . PASS . GT:GQ:BAF:LRR 0/0:0.518452:0.0:-0.193469 5 7886799 newrs147960130 C T . PASS . GT:GQ:BAF:LRR 0/0:0.517655:0.0116109848022:0.00421104 5 7895862 newrs147277149 C T . PASS . GT:GQ:BAF:LRR 0/0:0.496997:0.0:-0.0219137 +5 9136691 1KG_5_9136691 C CACAT . PASS . GT:GQ:BAF:LRR 0/0:0.423649:0.039069712162:0.176712 +5 9629611 1KG_5_9629611 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.515687:0.0:-0.0397244 +5 26890644 1KG_5_26890644 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.487384:0.0:-0.1039 5 32268852 newrs150354971 G A . PASS . GT:GQ:BAF:LRR 0/0:0.489312:0.0211846828461:-0.223896 5 34005987 newrs149566702 G A . PASS . GT:GQ:BAF:LRR 0/0:0.516492:0.0:-0.31821 +5 34914825 1KG_5_34914825 C CACTTT . PASS . GT:GQ:BAF:LRR 0/0:0.474853:0.0253323316574:0.0321093 5 34937509 newrs150576702 C T . PASS . GT:GQ:BAF:LRR 0/0:0.43061:0.0:-0.357641 +5 34954813 1KG_5_34954813 C CAGAT . PASS . GT:GQ:BAF:LRR 0/0:0.501857:0.0:0.186099 +5 35010225 1KG_5_35010225 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.757492:0.0:-0.0808874 5 36037996 newrs147315371 G A . PASS . GT:GQ:BAF:LRR 0/0:0.495417:0.0:0.0969049 5 37121858 newrs150242262 G A . PASS . GT:GQ:BAF:LRR 0/0:0.471498:0.0:-0.033777 5 37153889 newrs150273774 C A . PASS . GT:GQ:BAF:LRR 0/0:0.476623:0.00462007522583:-0.918966 +5 38438374 1KG_5_38438374 A AAG . PASS . GT:GQ:BAF:LRR 0/0:0.499191:0.0:-0.0328829 +5 39202844 1KG_5_39202844 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.432598:0.0:-0.0894916 +5 40852633 1KG_5_40852633 A AGTGC . PASS . GT:GQ:BAF:LRR 0/0:0.510234:0.0:-0.109318 +5 41176606 1KG_5_41176606 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.391052:0.0585982:0.0847711 5 41381928 newrs147819890 C T . PASS . GT:GQ:BAF:LRR 0/0:0.506588:0.0:-0.0765792 +5 52403010 1KG_5_52403010 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.163779 5 54456071 newrs148475851 G A . PASS . GT:GQ:BAF:LRR 0/0:0.511547:0.0:-0.134849 +5 54570545 1KG_5_54570545 A AT . PASS . GT:GQ:BAF:LRR 0/0:0.487014:0.0:0.160894 +5 63509552 1KG_5_63509552 A AT . PASS . GT:GQ:BAF:LRR 0/0:0.428318:0.0:0.125302 +5 64883178 1KG_5_64883178 T TA . PASS . GT:GQ:BAF:LRR 0/0:0.497512:0.0:0.285055 +5 65370909 1KG_5_65370909 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.500415:0.0:0.124178 5 68616173 newrs148555744 C T . PASS . GT:GQ:BAF:LRR 0/0:0.422314:0.0:0.113655 5 72419522 newrs149489778 C T . PASS . GT:GQ:BAF:LRR 0/0:0.484685:0.0:0.0821432 +5 72848631 1KG_5_72848631 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.493089:0.0:0.0203649 5 72850781 newrs150789725 G A . PASS . GT:GQ:BAF:LRR 0/0:0.503986:0.0:-0.0377243 +5 75936817 1KG_5_75936817 A AGAGTTGCTTCTTCGCTTTC . PASS . GT:GQ:BAF:LRR 0/0:0.482458:0.0:-0.118212 +5 76358966 1KG_5_76358966 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.496579:0.0:-0.430005 +5 77784900 1KG_5_77784900 A AT . PASS . GT:GQ:BAF:LRR 0/0:0.486569:0.0324705839157:0.0030239 +5 77805741 1KG_5_77805741 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.500038:0.00419592:-0.155919 +5 87536654 1KG_5_87536654 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.659416:0.0:-0.010797 +5 89933665 1KG_5_89933665 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.000610888004303:-0.0130493 5 89943581 newrs148097083 G A . PASS . GT:GQ:BAF:LRR 0/0:0.514086:0.0:0.00888062 +5 93798199 1KG_5_93798199 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.500103:0.0:0.280033 5 95152324 newrs146662850 G A . PASS . GT:GQ:BAF:LRR 0/0:0.262222:0.0215516090393:0.0030124 5 95761545 newrs146545244 C T . PASS . GT:GQ:BAF:LRR 0/0:0.479755:0.0151836872101:-0.0912683 5 96079442 newrs147728486 C T . PASS . GT:GQ:BAF:LRR 0/0:0.390289:0.0:0.0202716 5 96130793 newrs150415434 C A . PASS . GT:GQ:BAF:LRR 0/0:0.416686:0.00451338291168:0.00768689 +5 96315241 1KG_5_96315241 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.351044:0.00477834:-0.253944 +5 96363473 1KG_5_96363473 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.361837:0.0:-0.00421845 5 96512820 newrs150431916 C T . PASS . GT:GQ:BAF:LRR 0/0:0.499582:0.0240887403488:-0.285518 5 109181564 newrs147671879 A G . PASS . GT:GQ:BAF:LRR 0/0:0.500193:0.0:-0.400719 +5 111754653 1KG_5_111754653 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.451363:0.0:0.119019 5 121767699 newrs148152880 C T . PASS . GT:GQ:BAF:LRR 0/0:0.805341:0.0:-0.137478 +5 122734882 1KG_5_122734882 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.478358:0.0361764431:-0.33374 5 125894990 newrs148052962 G A . PASS . GT:GQ:BAF:LRR 0/0:0.4052:0.00488156080246:-0.0586135 5 127595252 newrs150258538 G T . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.0:0.05085 +5 130782221 1KG_5_130782221 T TCTC . PASS . GT:GQ:BAF:LRR 0/0:0.490143:0.0:0.135954 5 131822691 newrs146963938 G A . PASS . GT:GQ:BAF:LRR 0/0:0.431821:0.0:-0.000399141 5 132088556 newrs148377101 A G . PASS . GT:GQ:BAF:LRR 0/0:0.401343:0.000387462:-0.157524 +5 132197699 1KG_5_132197699 C CG . PASS . GT:GQ:BAF:LRR 0/0:0.410957:0.0154467:-1.0312 5 134305783 newrs149256453 G A . PASS . GT:GQ:BAF:LRR 0/0:0.517732:0.0:0.000592531 +5 135277240 1KG_5_135277240 GCT G . PASS . GT:GQ:BAF:LRR 0/0:0.869858:0.0:0.00855634 +5 137506174 1KG_5_137506174 A AT . PASS . GT:GQ:BAF:LRR 0/0:0.50761:0.0:-0.639506 5 137520544 newrs150082210 C T . PASS . GT:GQ:BAF:LRR 0/0:0.493274:0.0:-0.321731 +5 137726896 1KG_5_137726896 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.498937:0.00457161664963:-0.390819 5 138386706 newrs149242794 G A . PASS . GT:GQ:BAF:LRR 0/0:0.401577:0.0:-0.0261099 +5 140530050 1KG_5_140530050 G GACA . PASS . GT:GQ:BAF:LRR 0/0:0.503015:0.0:-0.228452 5 140603105 newrs147283704 C T . PASS . GT:GQ:BAF:LRR 0/0:0.51489:0.0:-0.283637 5 140625576 newrs146617445 G T . PASS . GT:GQ:BAF:LRR 0/0:0.519132:0.0:0.0242016 5 140699110 newrs147266787 G A . PASS . GT:GQ:BAF:LRR 0/0:0.429249:0.0:-0.0930003 +5 140730350 1KG_5_140730350 T TTC . PASS . GT:GQ:BAF:LRR 0/0:0.409735:0.0:0.0614266 +5 140754411 1KG_5_140754411 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.495607:0.0:-0.799501 +5 140801197 1KG_5_140801197 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.0164501 +5 141511399 1KG_5_141511399 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.442309:0.0233133:-0.683817 5 145483756 newrs147348129 C T . PASS . GT:GQ:BAF:LRR 0/0:0.499212:0.0:-0.104196 +5 145647319 1KG_5_145647319 T TA . PASS . GT:GQ:BAF:LRR 0/0:0.47692:0.0:-0.0515458 +5 147466054 1KG_5_147466054 G GAA . PASS . GT:GQ:BAF:LRR 0/0:0.260354:0.0988464355469:-0.759442 5 149310680 newrs146591309 G A . PASS . GT:GQ:BAF:LRR 0/0:0.4986:0.0:-0.165184 5 151304053 newrs146895517 A G . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.0:0.104102 +5 156535947 1KG_5_156535947 T TAGC . PASS . GT:GQ:BAF:LRR 0/0:0.154905:0.0477266:0.0178291 5 159821492 newrs149228364 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.167868 5 162902464 newrs146791423 G T . PASS . GT:GQ:BAF:LRR 0/0:0.518293:0.0:0.23307 +5 171337613 1KG_5_171337613 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.474359:0.0:0.067198 5 171849419 newrs147770326 C T . PASS . GT:GQ:BAF:LRR 0/0:0.41841:0.00467300415039:0.0520086 +5 172662021 1KG_5_172662021 C CTGT . PASS . GT:GQ:BAF:LRR 0/0:0.477183:0.0:0.0302443 +5 172750232 1KG_5_172750232 G GCAA . PASS . GT:GQ:BAF:LRR 0/0:0.490656:0.00872552394867:-0.236914 +5 176815175 1KG_5_176815175 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.498674:0.0:0.00197885 5 177576841 newrs149168003 T C . PASS . GT:GQ:BAF:LRR 0/0:0.376958:0.0:0.146319 5 178045649 newrs149761770 G A . PASS . GT:GQ:BAF:LRR 0/0:0.468639:0.0:0.0817839 +5 179264436 1KG_5_179264436 T TA . PASS . GT:GQ:BAF:LRR 0/0:0.510564:0.0:0.151174 +5 179320359 1KG_5_179320359 G GAGA . PASS . GT:GQ:BAF:LRR 0/0:0.508315:0.0:-0.104817 5 179674439 newrs147368192 G A . PASS . GT:GQ:BAF:LRR 0/0:0.485271:0.0:-0.361344 +5 180477253 1KG_5_180477253 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.46081:0.0:-0.20238 +5 180551593 1KG_5_180551593 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.477879:0.0412880182266:-0.492636 +5 180622204 1KG_5_180622204 C CAG . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.0395565 6 2838116 newrs150484232 C T . PASS . GT:GQ:BAF:LRR 0/0:0.498202:0.0:0.112473 6 2838782 newrs149196414 C T . PASS . GT:GQ:BAF:LRR 0/0:0.475714:0.0129316449165:-0.0603951 6 4126368 newrs146626003 C T . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.0346471 @@ -420,92 +759,176 @@ 6 6266983 newrs150249786 G A . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.00547230243683:0.0509329 6 7575014 newrs150339369 C T . PASS . GT:GQ:BAF:LRR 0/0:0.506698:0.00043797492981:0.100094 6 7605637 newrs149913039 C T . PASS . GT:GQ:BAF:LRR 0/0:0.451234:0.0:0.0831667 +6 10876226 1KG_6_10876226 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.467283:0.0:0.00389599 +6 13638121 1KG_6_13638121 T TTATTAC . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.00332695245743:0.142403 6 14135393 newrs149141188 C T . PASS . GT:GQ:BAF:LRR 0/0:0.410023:0.00212788581848:0.149121 6 16274728 newrs149938350 G A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:-0.0883985 6 17649394 newrs146704071 C T . PASS . GT:GQ:BAF:LRR 0/0:0.49999:0.0:-0.0675051 +6 24145907 1KG_6_24145907 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.498633:0.00504088401794:-0.0371919 6 24146082 newrs146546083 C T . PASS . GT:GQ:BAF:LRR 0/0:0.412921:0.0:0.225241 6 28200588 newrs147858031 C T . PASS . GT:GQ:BAF:LRR 0/0:0.486809:0.0:-0.124464 6 28966574 newrs149098069 G A . PASS . GT:GQ:BAF:LRR 0/0:0.517427:0.0:0.0762433 +6 29012322 1KG_6_29012322 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.878215:0.0:0.239417 +6 29054783 1KG_6_29054783 C CAT . PASS . GT:GQ:BAF:LRR 0/0:0.387556:0.0:0.0588639 6 29323270 newrs148190376 G A . PASS . GT:GQ:BAF:LRR 0/0:0.444712:0.000287234783173:-0.0283781 6 29638498 newrs150133803 C T . PASS . GT:GQ:BAF:LRR 0/0:0.514336:0.0:0.12948 +6 30558477 1KG_6_30558477 G GA . PASS . GT:GQ:BAF:LRR 0/1:0.819199:0.389173090458:-0.414735 +6 30572861 1KG_6_30572861 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.440469:0.0:-0.125936 +6 30613720 1KG_6_30613720 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.8492:0.0:-0.171443 6 31711970 newrs147515280 C T . PASS . GT:GQ:BAF:LRR 0/0:0.46247:0.0:-0.756938 6 33237519 newrs146797459 A G . PASS . GT:GQ:BAF:LRR 0/0:0.41844:0.0562754:-0.680694 +6 33283509 1KG_6_33283509 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.480601:0.0:-0.277433 +6 35424007 1KG_6_35424007 T TGGA . PASS . GT:GQ:BAF:LRR 0/0:0.411449:0.0:-0.0914871 6 35923138 newrs148376118 G A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.0301241 6 36044385 newrs150550578 C T . PASS . GT:GQ:BAF:LRR 0/0:0.402972:0.0:-0.0427638 +6 38652277 1KG_6_38652277 A AT . PASS . GT:GQ:BAF:LRR 0/0:0.509226:0.0:-0.0413598 6 38654668 newrs150725457 G A . PASS . GT:GQ:BAF:LRR 0/0:0.511761:0.0:-0.157295 +6 39286867 1KG_6_39286867 T TGC . PASS . GT:GQ:BAF:LRR 0/0:0.506797:0.0:-0.200944 6 39325151 newrs147669724 C T . PASS . GT:GQ:BAF:LRR 0/0:0.515761:0.0:-0.330397 6 39512364 newrs149018745 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.174162 +6 41001647 1KG_6_41001647 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.398554:0.0323064:-0.0200539 6 42689619 newrs146703538 T C . PASS . GT:GQ:BAF:LRR 0/0:0.73852:0.0:0.221439 +6 42981091 1KG_6_42981091 T TCTC . PASS . GT:GQ:BAF:LRR 0/0:0.361595:0.0:0.0847284 +6 43010588 1KG_6_43010588 A AT . PASS . GT:GQ:BAF:LRR 0/0:0.509501:0.0:-0.00802178 +6 43638654 1KG_6_43638654 G GAGA . PASS . GT:GQ:BAF:LRR 0/0:0.488944:0.0:0.0179955 6 44217441 newrs148434564 G A . PASS . GT:GQ:BAF:LRR 1/1:0.189612:0.929015055299:0.0806835 6 44376337 newrs148664123 C T . PASS . GT:GQ:BAF:LRR 0/0:0.473817:0.0:0.207414 +6 46830825 1KG_6_46830825 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.508181:0.0:-0.202566 +6 47650294 1KG_6_47650294 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.492541:0.0:0.0965073 6 49604373 newrs148576118 A C . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:0.091221 6 49665572 newrs147611117 C T . PASS . GT:GQ:BAF:LRR 0/0:0.467283:0.00373607873917:-0.00609951 6 49986840 newrs150306060 T C . PASS . GT:GQ:BAF:LRR 0/0:0.361595:0.0:-0.366178 6 51524480 newrs148617572 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.0556861 6 51612695 newrs146649803 C A . PASS . GT:GQ:BAF:LRR 0/0:0.430716:0.0624964237213:-0.62797 +6 51613120 1KG_6_51613120 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.401573:0.0:0.0305506 6 51944754 newrs149841071 C T . PASS . GT:GQ:BAF:LRR 0/0:0.513663:0.0:0.0043441 6 54245326 newrs147405762 G A . PASS . GT:GQ:BAF:LRR 0/0:0.348161:0.0:0.02333 +6 54805269 newrs148485145 CTTAAA C . PASS . GT:GQ:BAF:LRR 0/0:0.412812:0.0:0.0189654 6 56031702 newrs149344559 A C . PASS . GT:GQ:BAF:LRR 0/0:0.499112:0.0189819:-0.921558 +6 56422200 1KG_6_56422200 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.49268:0.00301742553711:0.041661 +6 62442612 1KG_6_62442612 T TATC . PASS . GT:GQ:BAF:LRR 0/0:0.494349:0.0:0.128638 6 70745831 newrs148417796 T G . PASS . GT:GQ:BAF:LRR 0/0:0.499281:0.0:-0.143673 6 70886456 newrs149084573 G A . PASS . GT:GQ:BAF:LRR 0/0:0.518369:0.0:-0.187747 6 71235565 newrs147626858 A G . PASS . GT:GQ:BAF:LRR 0/0:0.446692:0.0:0.246924 +6 74477869 1KG_6_74477869 G GTGTAA . PASS . GT:GQ:BAF:LRR 0/0:0.896098:0.0:-0.153326 +6 74520846 1KG_6_74520846 C CCG . PASS . GT:GQ:BAF:LRR 0/0:0.361595:0.00327854:-0.145157 +6 76024229 1KG_6_76024229 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.480484:0.0189352:-0.4754 +6 79695098 1KG_6_79695098 C CTCT . PASS . GT:GQ:BAF:LRR 0/0:0.5151:0.00271201133728:0.0482061 6 79735234 newrs150666163 A C . PASS . GT:GQ:BAF:LRR 0/0:0.502405:0.00637529:-0.204842 +6 80751896 1KG_6_80751896 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.491697:0.0:-0.00675216 6 80878661 newrs149766077 C T . PASS . GT:GQ:BAF:LRR 0/0:0.511074:0.00449514389038:0.0435437 +6 83851746 1KG_6_83851746 A AAAC . PASS . GT:GQ:BAF:LRR 0/0:0.511841:0.0:0.0803111 +6 87994592 1KG_6_87994592 T TACTCC . PASS . GT:GQ:BAF:LRR 0/0:0.300293:0.0:0.243098 +6 87994592 newrs148385063 TACTCC T . PASS . GT:GQ:BAF:LRR 0/0:0.767277:0.0:0.097701 6 88128008 newrs150688579 C A . PASS . GT:GQ:BAF:LRR 0/0:0.48702:0.00954270362854:0.0114397 6 88854927 newrs148575019 C T . PASS . GT:GQ:BAF:LRR 0/0:0.405282:0.0183826088905:0.0457113 +6 90402833 1KG_6_90402833 A AATTATCC . PASS . GT:GQ:BAF:LRR 0/0:0.495984:0.0:1.04383 +6 91226373 1KG_6_91226373 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.456159:0.00741535425186:0.192254 6 97726724 newrs149389562 C T . PASS . GT:GQ:BAF:LRR 0/0:0.511947:0.0:-1.0419 +6 99936669 1KG_6_99936669 C CAA . PASS . GT:GQ:BAF:LRR 0/0:0.504289:0.0:0.00787351 6 101246588 newrs149330987 C T . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.22692 +6 109802289 1KG_6_109802289 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.31509:0.0606482028961:-0.0904039 6 110083316 newrs149991846 C T . PASS . GT:GQ:BAF:LRR 0/0:0.514177:0.0:0.0147441 +6 110991663 1KG_6_110991663 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.440764:0.0:-0.0324704 +6 111628607 1KG_6_111628607 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.436136:0.0329877:-1.00623 +6 111694052 1KG_6_111694052 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.410406:0.00529611110687:-0.242232 6 116381238 newrs148677068 C T . PASS . GT:GQ:BAF:LRR 0/0:0.444153:0.0:0.0649031 +6 116442924 1KG_6_116442924 C CTCCTGGTTT . PASS . GT:GQ:BAF:LRR 0/0:0.484895:0.0:-0.0407234 +6 117128014 1KG_6_117128014 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.516479:0.0:-0.721152 6 117130477 newrs148056762 C T . PASS . GT:GQ:BAF:LRR 0/0:0.51585:0.00232928991318:0.196313 6 117714485 newrs150002762 C T . PASS . GT:GQ:BAF:LRR 0/0:0.460902:0.0:0.153582 +6 117859903 1KG_6_117859903 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.409945:0.0594654:-0.78227 6 126342411 newrs147290904 G A . PASS . GT:GQ:BAF:LRR 0/0:0.488048:0.0:-0.0512607 +6 127767595 1KG_6_127767595 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.348498:0.00431261:0.0465868 6 129591829 newrs149896793 G T . PASS . GT:GQ:BAF:LRR 0/0:0.879453:0.0:-0.0549465 6 129823916 newrs149210847 G A . PASS . GT:GQ:BAF:LRR 0/0:0.443605:0.0:-0.0520813 +6 130154692 1KG_6_130154692 C CACAA . PASS . GT:GQ:BAF:LRR 0/0:0.516798:0.0:0.0178121 6 131903787 newrs146625637 G A . PASS . GT:GQ:BAF:LRR 0/0:0.477381:0.0:-0.46777 6 131917198 newrs150404447 G A . PASS . GT:GQ:BAF:LRR ./.:0.147684:0.0924681425095:-0.537138 6 131971260 newrs148423655 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.305997 6 132860014 newrs148058947 C T . PASS . GT:GQ:BAF:LRR 0/0:0.765983:2.89082527161e-05:0.120775 6 133072307 newrs148308586 G A . PASS . GT:GQ:BAF:LRR 0/0:0.393705:0.0:0.119613 6 133091438 newrs147790535 G A . PASS . GT:GQ:BAF:LRR 0/0:0.499844:0.00934100151062:-0.197474 +6 133118182 1KG_6_133118182 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.338856:0.0:-0.333478 6 135644371 newrs148000791 T C . PASS . GT:GQ:BAF:LRR 0/0:0.769926:0.00590789:-0.0474465 +6 136913666 1KG_6_136913666 T TGTC . PASS . GT:GQ:BAF:LRR 0/0:0.812341:0.0:-0.360944 6 144167206 newrs147204809 C T . PASS . GT:GQ:BAF:LRR 0/0:0.361595:0.000106871128082:0.0918177 +6 144769846 1KG_6_144769846 G GCCT . PASS . GT:GQ:BAF:LRR 0/0:0.315006:0.0:0.00330842 +6 148792600 1KG_6_148792600 C CG . PASS . GT:GQ:BAF:LRR 0/0:0.513169:0.0:-0.100991 6 150067220 newrs149249345 C T . PASS . GT:GQ:BAF:LRR 0/0:0.829428:0.0163365602493:-0.467624 6 151142369 newrs147160033 G A . PASS . GT:GQ:BAF:LRR 0/0:0.470049:0.0:-0.0240805 6 151198963 newrs148145283 G A . PASS . GT:GQ:BAF:LRR 0/0:0.495932:0.0016867518425:0.18917 +6 151674312 1KG_6_151674312 A AAAG . PASS . GT:GQ:BAF:LRR 0/0:0.42295:0.00281874:-0.437766 6 159086426 newrs149940898 G A . PASS . GT:GQ:BAF:LRR 0/0:0.496902:0.0:-0.173953 +6 159134910 1KG_6_159134910 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.415202:0.0:0.00617898 6 160206506 newrs147224137 C A . PASS . GT:GQ:BAF:LRR 0/0:0.517088:0.0:0.142711 6 166576109 newrs146708556 C T . PASS . GT:GQ:BAF:LRR 0/0:0.472919:0.0:0.069307 +7 2646794 1KG_7_2646794 C CAGG . PASS . GT:GQ:BAF:LRR 0/0:0.49782:0.0:-0.0859827 +7 4841605 1KG_7_4841605 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.497581:0.0:0.344804 7 6094176 newrs148495208 C T . PASS . GT:GQ:BAF:LRR 0/0:0.494974:0.0:0.218663 7 7398347 newrs148652610 G A . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:-0.0484772 7 7420436 newrs146560754 C A . PASS . GT:GQ:BAF:LRR 0/0:0.498756:0.0:-0.837225 +7 16298017 1KG_7_16298017 A AAAC . PASS . GT:GQ:BAF:LRR 0/0:0.483202:0.0:-0.311472 7 16901072 newrs147702108 C T . PASS . GT:GQ:BAF:LRR 0/0:0.503938:0.0:0.0794229 7 20687233 newrs150279505 C T . PASS . GT:GQ:BAF:LRR 0/0:0.626366:0.0:0.052956 7 20795056 newrs146527949 C T . PASS . GT:GQ:BAF:LRR 0/0:0.823854:0.0:0.171989 7 21760479 newrs149364992 G A . PASS . GT:GQ:BAF:LRR 0/0:0.512487:0.0:-0.0419911 +7 27181455 1KG_7_27181455 C CAG . PASS . GT:GQ:BAF:LRR 0/0:0.511852:0.0:-0.343514 +7 30058726 1KG_7_30058726 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.263519:0.0:-0.155466 +7 30671937 1KG_7_30671937 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.374873:0.0:0.0862052 7 31015394 newrs146944568 G T . PASS . GT:GQ:BAF:LRR 0/0:0.498177:0.0:-0.221978 7 31682773 newrs147656859 C T . PASS . GT:GQ:BAF:LRR 0/0:0.376958:0.00934475660324:0.0268844 +7 34097760 1KG_7_34097760 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.123122 7 37953975 newrs146871972 C T . PASS . GT:GQ:BAF:LRR 0/0:0.438034:0.0:-0.136432 +7 38500935 1KG_7_38500935 C CTGA . PASS . GT:GQ:BAF:LRR 0/0:0.510067:0.0:0.0393055 +7 40228131 1KG_7_40228131 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.503295:0.0:-0.941211 +7 44524798 1KG_7_44524798 T TA . PASS . GT:GQ:BAF:LRR 0/0:0.454746:0.0:-0.0399719 +7 47408711 1KG_7_47408711 G GTGAA . PASS . GT:GQ:BAF:LRR 0/0:0.508963:0.0:-0.322867 +7 47894539 1KG_7_47894539 C CTG . PASS . GT:GQ:BAF:LRR 0/0:0.507323:0.0:-0.0772181 +7 47942051 1KG_7_47942051 T TA . PASS . GT:GQ:BAF:LRR 0/0:0.515893:0.00616210699081:0.148291 +7 47969063 1KG_7_47969063 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.426745:0.0:-0.0851789 +7 48033969 1KG_7_48033969 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.467283:0.0127591:-0.179565 7 48068485 newrs146974310 G T . PASS . GT:GQ:BAF:LRR 0/0:0.504407:0.0:-0.946155 +7 48556401 1KG_7_48556401 T TA . PASS . GT:GQ:BAF:LRR 0/0:0.432141:0.0123199224472:-0.129124 7 66458309 newrs148500031 T G . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.0:0.0321762 +7 70249962 1KG_7_70249962 A ACCT . PASS . GT:GQ:BAF:LRR 0/0:0.500042:0.0:0.0319598 7 72745738 newrs147213094 C T . PASS . GT:GQ:BAF:LRR 0/0:0.876565:0.0:-0.0771317 +7 73752807 1KG_7_73752807 C CCCT . PASS . GT:GQ:BAF:LRR 0/0:0.368358:0.0:0.183067 +7 73771743 1KG_7_73771743 A AGGCCAC . PASS . GT:GQ:BAF:LRR 0/0:0.518772:0.0:-0.17229 +7 76132781 1KG_7_76132781 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.224305:0.0:0.0760656 +7 76903028 1KG_7_76903028 A AGAT . PASS . GT:GQ:BAF:LRR 0/0:0.514619:0.0:-0.300149 +7 77408478 1KG_7_77408478 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.490337:0.0:-0.792393 7 78150747 newrs146782279 C T . PASS . GT:GQ:BAF:LRR 0/0:0.498423:0.0:0.0804179 7 83606448 newrs149706425 C T . PASS . GT:GQ:BAF:LRR 0/0:0.496814:0.0:0.146361 7 87053223 newrs147134978 G A . PASS . GT:GQ:BAF:LRR 0/0:0.424438:0.00156581401825:0.146698 +7 87074281 1KG_7_87074281 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.483482:0.0:-0.122703 +7 87081084 1KG_7_87081084 A AT . PASS . GT:GQ:BAF:LRR 0/0:0.444662:0.0399671792984:-0.18216 7 89856411 newrs148055758 C T . PASS . GT:GQ:BAF:LRR ./.:0.034817:0.109675884247:0.144389 +7 89982305 1KG_7_89982305 G GAGTA . PASS . GT:GQ:BAF:LRR 0/0:0.453143:0.0174778699875:-0.105307 +7 90042394 1KG_7_90042394 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.421596:0.0:-0.142066 +7 91855118 1KG_7_91855118 T TCTTC . PASS . GT:GQ:BAF:LRR 0/0:0.514307:0.0:-0.00946518 +7 91924374 1KG_7_91924374 C CCT . PASS . GT:GQ:BAF:LRR 0/0:0.49655:0.0:0.0303893 +7 91936913 1KG_7_91936913 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.497215:0.0:-0.325869 7 92147282 newrs149806989 G A . PASS . GT:GQ:BAF:LRR 0/0:0.470185:0.0:0.0028629 7 92734725 newrs147146654 G T . PASS . GT:GQ:BAF:LRR 0/0:0.461277:0.0:0.065138 +7 92761060 1KG_7_92761060 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.498843:0.0:-0.0993634 7 93125288 newrs148624177 T C . PASS . GT:GQ:BAF:LRR 0/0:0.862597:0.00648627:-0.271906 7 94947635 newrs149100710 C T . PASS . GT:GQ:BAF:LRR 0/0:0.419162:0.0:0.164907 7 98951744 newrs150004356 A G . PASS . GT:GQ:BAF:LRR 0/0:0.85023:0.0431999:-0.057032 7 99021454 newrs147029104 C A . PASS . GT:GQ:BAF:LRR 0/0:0.376958:0.0:0.0332874 7 99056770 newrs146584377 T G . PASS . GT:GQ:BAF:LRR 0/0:0.310014:0.0151878:0.107117 +7 99364034 1KG_7_99364034 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.492444:0.0:0.075034 7 99447238 newrs146587177 C T . PASS . GT:GQ:BAF:LRR 0/0:0.479159:0.0050385594368:-0.0913506 7 99461224 newrs149091175 C T . PASS . GT:GQ:BAF:LRR 0/0:0.412935:0.0155234336853:0.008036 +7 99801714 1KG_7_99801714 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.494655:0.00226426124573:-0.0580427 +7 100320750 1KG_7_100320750 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.431119:0.0:-0.10377 7 100682921 newrs148241944 C T . PASS . GT:GQ:BAF:LRR 0/0:0.49213:0.0:-0.00512057 7 100701287 newrs148704443 C T . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.132494 7 102572363 newrs149803390 G A . PASS . GT:GQ:BAF:LRR 0/0:0.466583:0.0368211269379:-0.0119469 7 103194107 newrs149473868 G A . PASS . GT:GQ:BAF:LRR 0/0:0.497895:0.0:-0.288528 +7 104742018 1KG_7_104742018 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.367991:0.0977408:-0.446335 +7 104753240 1KG_7_104753240 A ACCC . PASS . GT:GQ:BAF:LRR 0/0:0.375612:0.0:-0.0878141 +7 105189137 1KG_7_105189137 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.00407612323761:0.100892 7 107330644 newrs147952620 C T . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.0744032 7 107389484 newrs147566750 G A . PASS . GT:GQ:BAF:LRR 0/0:0.500344:0.0:0.0364388 7 107571875 newrs150279683 G A . PASS . GT:GQ:BAF:LRR 0/0:0.510223:0.0:-0.191995 @@ -516,151 +939,320 @@ 7 120972020 newrs148077060 T C . PASS . GT:GQ:BAF:LRR 0/0:0.472943:0.0:0.224081 7 122338300 newrs150520039 G A . PASS . GT:GQ:BAF:LRR 0/0:0.411296:0.0:-0.202642 7 128049368 newrs147481910 G A . PASS . GT:GQ:BAF:LRR 0/0:0.494525:0.00300014019012:-0.3465 +7 128784896 1KG_7_128784896 C CTCT . PASS . GT:GQ:BAF:LRR 0/0:0.500047:0.0:0.121404 7 129102806 newrs150375291 G A . PASS . GT:GQ:BAF:LRR 0/0:0.39855:0.0:0.0763563 7 130140359 newrs150557584 T C . PASS . GT:GQ:BAF:LRR 0/0:0.371084:0.0:0.0972567 7 130297018 newrs149067956 A C . PASS . GT:GQ:BAF:LRR 0/0:0.402212:0.0:-0.0416476 7 134346603 newrs149329328 G A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:-0.058507 7 134743986 newrs148387846 G A . PASS . GT:GQ:BAF:LRR 0/0:0.517484:0.0:0.16241 +7 135098341 1KG_7_135098341 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.514547:0.0:0.00631358 7 138453918 newrs146911574 G A . PASS . GT:GQ:BAF:LRR 0/0:0.517328:0.0:0.00369581 7 140037084 newrs150070842 C A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.000719308853149:0.0970307 7 141957488 newrs149822174 C T . PASS . GT:GQ:BAF:LRR 0/0:0.449554:0.00251418352127:0.0227259 7 142723442 newrs147956738 G A . PASS . GT:GQ:BAF:LRR 0/0:0.416461:0.0:0.0851405 +7 143055970 1KG_7_143055970 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.483192:0.00713151:-0.217443 +7 143141019 1KG_7_143141019 AT A . PASS . GT:GQ:BAF:LRR 0/0:0.421532:0.000646301:-0.844542 +7 150389837 1KG_7_150389837 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.437041:0.0288665:-0.302916 +7 150748955 1KG_7_150748955 C CAGA . PASS . GT:GQ:BAF:LRR 0/0:0.460229:0.0:0.183907 +7 151664477 1KG_7_151664477 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.461881:0.0:-0.209579 7 151704910 newrs148226163 A G . PASS . GT:GQ:BAF:LRR 0/0:0.418337:0.0:0.123419 +7 154745994 1KG_7_154745994 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.499582:0.0:-0.0334299 7 156516874 newrs148655712 T C . PASS . GT:GQ:BAF:LRR 0/0:0.508644:0.0:0.0939681 +8 1851668 1KG_8_1851668 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.90055:0.00536489486694:0.0335635 +8 2813271 1KG_8_2813271 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.469594:0.0:-0.143859 +8 6378797 1KG_8_6378797 A AT . PASS . GT:GQ:BAF:LRR 0/0:0.494943:0.0231835842133:-1.64324 8 6728244 newrs148577927 G A . PASS . GT:GQ:BAF:LRR 0/0:0.48212:0.0:-0.062812 +8 17123459 1KG_8_17123459 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.487384:0.0:0.0589699 8 17412208 newrs149207619 G A . PASS . GT:GQ:BAF:LRR 0/0:0.385962:0.0171897411346:0.00994784 +8 17726080 1KG_8_17726080 A ATCT . PASS . GT:GQ:BAF:LRR 0/0:0.474353:0.00192850828171:0.122849 +8 19250997 1KG_8_19250997 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.429086:0.0:0.0415878 8 19819645 newrs149089920 G A . PASS . GT:GQ:BAF:LRR 0/0:0.50382:0.0:0.110698 +8 22463615 1KG_8_22463615 C CT . PASS . GT:GQ:BAF:LRR ./.:0.0231232:0.29464495182:-0.478227 +8 25250353 1KG_8_25250353 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.0611467 +8 25257506 1KG_8_25257506 T TAC . PASS . GT:GQ:BAF:LRR 0/0:0.419663:0.0:-0.109244 8 29923547 newrs149135189 A C . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.0941432 8 29924293 newrs150321308 C T . PASS . GT:GQ:BAF:LRR 0/0:0.431675:0.0:0.150147 +8 30700805 1KG_8_30700805 TGTGA T . PASS . GT:GQ:BAF:LRR 0/0:0.514867:0.0:0.286332 +8 30703366 1KG_8_30703366 T TTTTC . PASS . GT:GQ:BAF:LRR 0/0:0.514277:0.0:0.22352 +8 30704971 1KG_8_30704971 G GTCC . PASS . GT:GQ:BAF:LRR 0/0:0.500204:0.0:-0.0194862 +8 36925268 1KG_8_36925268 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.0:0.0710687 +8 38005729 1KG_8_38005729 C CCTT . PASS . GT:GQ:BAF:LRR 0/0:0.445463:0.0:-0.0315662 +8 38839282 1KG_8_38839282 GAA G . PASS . GT:GQ:BAF:LRR 0/0:0.513399:0.0:0.0126244 8 55013468 newrs146719663 C T . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:0.0428714 8 59720335 newrs148474393 G A . PASS . GT:GQ:BAF:LRR 0/0:0.491209:0.0:0.00992137 8 62559438 newrs148798777 C T . PASS . GT:GQ:BAF:LRR 0/0:0.390176:0.0360451936722:-0.316261 +8 67361182 1KG_8_67361182 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.475875:0.00289988517761:0.110341 +8 68070697 1KG_8_68070697 CAA C . PASS . GT:GQ:BAF:LRR 0/0:0.430687:0.0145558:-0.066467 +8 70514025 1KG_8_70514025 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.498311:0.0:-0.196001 +8 70541784 1KG_8_70541784 G GAAC . PASS . GT:GQ:BAF:LRR 0/0:0.499882:0.0:0.0773748 +8 87235305 1KG_8_87235305 A ATTG . PASS . GT:GQ:BAF:LRR 0/0:0.514767:0.00411711:-0.376377 8 92378808 newrs149167044 G T . PASS . GT:GQ:BAF:LRR 0/0:0.487412:0.0348261594772:-1.02679 8 94809573 newrs150332116 C T . PASS . GT:GQ:BAF:LRR 0/0:0.47997:0.0:-0.148844 +8 95423442 1KG_8_95423442 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.196957 8 95780690 newrs147961118 C T . PASS . GT:GQ:BAF:LRR 0/0:0.512505:0.0:-0.740395 8 98817694 newrs146674780 T G . PASS . GT:GQ:BAF:LRR 0/0:0.477981:0.0:-0.183789 +8 99006776 1KG_8_99006776 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.435208:0.0114983:-0.114152 8 99153059 newrs149102421 C T . PASS . GT:GQ:BAF:LRR 0/0:0.516508:0.0:-0.0896263 +8 100880519 1KG_8_100880519 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.381082:0.0:-0.039154 +8 101282222 1KG_8_101282222 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.467283:0.0:0.165253 +8 101608881 1KG_8_101608881 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.466416:0.0:-0.128787 8 105360974 newrs149253106 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.0334924 +8 106646509 1KG_8_106646509 T TGG . PASS . GT:GQ:BAF:LRR 0/0:0.467283:0.0:0.0514753 +8 109240542 1KG_8_109240542 G GGT . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.0747104 +8 109797183 1KG_8_109797183 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.467283:0.0:-0.523691 +8 110447527 1KG_8_110447527 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.514585:0.0:-0.166139 8 113243773 newrs148762244 C T . PASS . GT:GQ:BAF:LRR 0/0:0.496741:0.0:0.0121333 8 113529404 newrs149308903 G A . PASS . GT:GQ:BAF:LRR 0/0:0.406537:0.0889647006989:-0.634537 8 120079545 newrs149010496 C T . PASS . GT:GQ:BAF:LRR 0/0:0.5093:0.0:-0.0297208 8 121528432 newrs146791881 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.00410368 8 124153064 newrs147736638 C T . PASS . GT:GQ:BAF:LRR 0/0:0.50028:0.00956904888153:-0.0463144 +8 124340761 1KG_8_124340761 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.507909:0.0:-0.0980146 8 125988753 newrs146924154 G A . PASS . GT:GQ:BAF:LRR 0/0:0.511391:0.00474852323532:-0.186399 8 125989242 newrs147804097 T G . PASS . GT:GQ:BAF:LRR 0/0:0.528154:0.0:0.0763266 8 126091058 newrs150749307 A C . PASS . GT:GQ:BAF:LRR 0/0:0.409735:0.0:0.0371055 8 131793034 newrs150698439 G A . PASS . GT:GQ:BAF:LRR 0/0:0.40745:0.00228369235992:-0.145221 8 133045281 newrs150715638 C T . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.00408619 +8 133067287 newrs150127981 AG A . PASS . GT:GQ:BAF:LRR 0/0:0.832771:0.0:0.085993 +8 133919117 1KG_8_133919117 A ACAGCTGCCT . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:0.0370353 8 139647253 newrs147655243 T C . PASS . GT:GQ:BAF:LRR 0/0:0.496736:0.0:-0.095211 8 141828445 newrs149643582 C T . PASS . GT:GQ:BAF:LRR 0/0:0.429057:0.0:0.0567128 +8 142154280 1KG_8_142154280 T TGAAGTG . PASS . GT:GQ:BAF:LRR 0/0:0.447652:0.0:0.0402365 +8 142161936 1KG_8_142161936 G GGTTA . PASS . GT:GQ:BAF:LRR 0/0:0.885451:0.0:-0.231565 8 143922641 newrs150041552 C T . PASS . GT:GQ:BAF:LRR 0/0:0.379684:0.0:0.102652 +8 144413499 1KG_8_144413499 C CCTT . PASS . GT:GQ:BAF:LRR 0/0:0.475594:0.00364196300507:0.123967 +8 144890811 1KG_8_144890811 C CCTT . PASS . GT:GQ:BAF:LRR 0/0:0.488144:0.0:0.107807 8 145541643 newrs149913927 G A . PASS . GT:GQ:BAF:LRR 0/0:0.501834:0.0:0.341797 +9 712040 1KG_9_712040 C CAGCTGT . PASS . GT:GQ:BAF:LRR 0/0:0.724221:0.00312185287476:-0.0197657 9 730250 newrs149121553 T G . PASS . GT:GQ:BAF:LRR 0/0:0.443413:0.0:0.0804472 +9 6506088 1KG_9_6506088 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.0355517 9 6620265 newrs147066809 C T . PASS . GT:GQ:BAF:LRR 0/0:0.498822:0.000689148902893:-0.0930856 9 12695801 newrs147425437 C T . PASS . GT:GQ:BAF:LRR 0/0:0.49518:0.0:0.00874371 9 14313479 newrs149244411 A G . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:0.172245 +9 14808065 1KG_9_14808065 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.37696:0.0:-0.0364775 9 15189604 newrs150307895 G A . PASS . GT:GQ:BAF:LRR 0/0:0.460868:0.0:-0.0418732 9 15777824 newrs150773145 G A . PASS . GT:GQ:BAF:LRR 0/0:0.507443:0.0:-0.245318 +9 19300187 1KG_9_19300187 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.498949:0.0:-0.279299 +9 21409708 1KG_9_21409708 C CAAT . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.00442814826965:0.0816068 9 23704916 newrs149957439 C T . PASS . GT:GQ:BAF:LRR 0/0:0.409735:0.0:0.127377 9 32418196 newrs150497498 G T . PASS . GT:GQ:BAF:LRR 0/0:0.391281:0.00188255310059:0.0385714 +9 32457307 1KG_9_32457307 C CAGAA . PASS . GT:GQ:BAF:LRR 0/0:0.510389:0.0:0.00265486 +9 32541745 1KG_9_32541745 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.487384:0.0:-0.0341349 +9 33295379 1KG_9_33295379 C CCG . PASS . GT:GQ:BAF:LRR 0/0:0.321756:0.0:0.202574 +9 34106467 1KG_9_34106467 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.513669:2.16960906982e-05:-0.42546 +9 35059126 1KG_9_35059126 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:-0.206289 9 35105838 newrs150293710 T C . PASS . GT:GQ:BAF:LRR 0/0:0.374745:0.015341:-0.344273 9 36229085 newrs150132839 G A . PASS . GT:GQ:BAF:LRR 0/0:0.463932:0.0:0.0214163 9 36246023 newrs150714953 C T . PASS . GT:GQ:BAF:LRR 0/0:0.452542:0.0:-0.05807 9 36599448 newrs149686898 G T . PASS . GT:GQ:BAF:LRR 0/0:0.498642:0.00392311811447:-0.0183786 +9 37304189 1KG_9_37304189 A AGATAGCTAATAACCG . PASS . GT:GQ:BAF:LRR 0/0:0.310014:0.041352:-0.0362195 +9 37515947 1KG_9_37515947 G GGTT . PASS . GT:GQ:BAF:LRR 0/0:0.456594:0.0:-0.872505 +9 38396320 1KG_9_38396320 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.483202:0.0:0.00644628 9 71842791 newrs146543810 T C . PASS . GT:GQ:BAF:LRR 0/0:0.483202:0.0194993:-0.407073 +9 71864336 1KG_9_71864336 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.485728:0.0:-0.265432 9 72090963 newrs146989913 C T . PASS . GT:GQ:BAF:LRR 0/0:0.39031:0.00765013694763:0.110792 9 80049440 newrs148017027 T C . PASS . GT:GQ:BAF:LRR 0/0:0.37316:0.0:-0.778066 9 88694215 newrs150427559 C A . PASS . GT:GQ:BAF:LRR 0/0:0.837281:0.0:-0.505544 9 90584745 newrs150288403 C T . PASS . GT:GQ:BAF:LRR 0/0:0.438569:0.0:-0.173952 +9 95177620 1KG_9_95177620 A AAT . PASS . GT:GQ:BAF:LRR 0/0:0.500604:0.0:0.195804 9 95236930 newrs148382623 G A . PASS . GT:GQ:BAF:LRR 0/0:0.517606:0.0:-0.0564555 9 99150527 newrs149972653 G A . PASS . GT:GQ:BAF:LRR 0/0:0.507227:0.0:-0.194281 +9 99304164 1KG_9_99304164 AG A . PASS . GT:GQ:BAF:LRR 0/0:0.500128:0.0:-0.0942302 9 99521480 newrs148296433 G T . PASS . GT:GQ:BAF:LRR 0/0:0.320932:0.0:-0.0681799 9 101611350 newrs146530383 G A . PASS . GT:GQ:BAF:LRR 0/0:0.516196:0.0:0.0148138 9 103027123 newrs149055711 G A . PASS . GT:GQ:BAF:LRR 0/0:0.491606:0.0:-0.704742 9 103035281 newrs148239569 C A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.000614404678345:0.011245 9 104153053 newrs150313404 G A . PASS . GT:GQ:BAF:LRR 0/0:0.310014:0.0:0.275689 +9 108366764 1KG_9_108366764 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:0.0601922 +9 111681540 1KG_9_111681540 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.366952:0.0124192:0.0247898 9 114090454 newrs147330382 G T . PASS . GT:GQ:BAF:LRR 0/0:0.499408:0.0:-0.00693784 9 115811718 newrs149489774 C T . PASS . GT:GQ:BAF:LRR 0/0:0.496922:0.0143982172012:-0.0371306 9 116082637 newrs148709910 C T . PASS . GT:GQ:BAF:LRR 0/0:0.445186:0.0:0.111948 +9 116183462 1KG_9_116183462 A AAGAG . PASS . GT:GQ:BAF:LRR 0/0:0.486345:0.00237401:-0.10334 9 117066858 newrs148603511 C T . PASS . GT:GQ:BAF:LRR 0/0:0.898204:0.0:-0.0691764 9 123779921 newrs149506797 C T . PASS . GT:GQ:BAF:LRR 0/0:0.479659:0.0:0.0266884 +9 124080725 1KG_9_124080725 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.466715:0.0218145:-0.759269 +9 125054114 1KG_9_125054114 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.373443:0.00239436:0.0020424 9 125377927 newrs147488616 G A . PASS . GT:GQ:BAF:LRR 0/0:0.489495:0.0:-0.0757379 +9 125391770 1KG_9_125391770 C CA . PASS . GT:GQ:BAF:LRR 1/1:0.916879:1.0:-0.135879 +9 125562930 1KG_9_125562930 CACTTCTTCTGTGACCA C . PASS . GT:GQ:BAF:LRR 0/0:0.425267:0.0:-0.184481 9 128118071 newrs149182108 C T . PASS . GT:GQ:BAF:LRR 0/0:0.446959:0.0:-0.208093 +9 131196467 1KG_9_131196467 G GATGGAGGAT . PASS . GT:GQ:BAF:LRR 0/0:0.498829:0.0:0.151566 9 131495705 newrs148330265 C A . PASS . GT:GQ:BAF:LRR 0/0:0.437462:0.000301659107208:0.0410152 9 131720291 newrs147379666 A C . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.085527 9 133578458 newrs149299789 C T . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.00654429197311:0.0245837 9 133993305 newrs146631291 T G . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.0629581 +9 134070657 1KG_9_134070657 T TCTTCTAATTTCA . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:0.125039 +9 134072668 1KG_9_134072668 C CCTT . PASS . GT:GQ:BAF:LRR 0/0:0.517908:0.0:0.0303974 9 135153507 newrs148041889 T C . PASS . GT:GQ:BAF:LRR 0/0:0.49797:0.0:0.0785968 +9 135940549 1KG_9_135940549 A AACGTCATCGTGGTC . PASS . GT:GQ:BAF:LRR 0/0:0.511042:0.00611056:-0.129143 9 136219551 newrs147816470 G A . PASS . GT:GQ:BAF:LRR 0/0:0.474548:0.00285243988037:0.0567933 +9 136268037 1KG_9_136268037 A ACGCTGGGC . PASS . GT:GQ:BAF:LRR 0/0:0.432436:0.0590757:-1.23507 +9 139407931 1KG_9_139407931 C CATT . PASS . GT:GQ:BAF:LRR 0/0:0.39027:0.0:1.15047 +9 140441314 1KG_9_140441314 C CTT . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:0.215119 +10 1066786 1KG_10_1066786 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.504784:0.0:-0.0582496 10 7774310 newrs146878856 C T . PASS . GT:GQ:BAF:LRR 0/0:0.412484:0.0:-0.047972 10 11908528 newrs148477384 A C . PASS . GT:GQ:BAF:LRR 0/0:0.399871:0.0:0.0159494 +10 12259383 1KG_10_12259383 T TA . PASS . GT:GQ:BAF:LRR 0/0:0.510862:0.0:0.230785 10 13639535 newrs150642801 G A . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:0.0228095 +10 15902261 1KG_10_15902261 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.000718712806702:-0.222043 10 17113425 newrs149242963 C A . PASS . GT:GQ:BAF:LRR 0/0:0.514945:0.0:-0.0432116 +10 17686345 1KG_10_17686345 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.496281:0.0:-0.0452626 10 21120157 newrs149647815 G A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.0329142 +10 23326364 1KG_10_23326364 A ATGAAGT . PASS . GT:GQ:BAF:LRR 0/0:0.4934:0.0:-0.0361889 +10 24813313 1KG_10_24813313 A ATGG . PASS . GT:GQ:BAF:LRR 0/0:0.409735:0.0:-0.014965 10 24880816 newrs148522047 G A . PASS . GT:GQ:BAF:LRR 0/0:0.497071:0.0:0.141646 +10 25312661 1KG_10_25312661 C CAGAT . PASS . GT:GQ:BAF:LRR 0/0:0.513192:0.0:0.284003 10 27508651 newrs150476576 C T . PASS . GT:GQ:BAF:LRR 0/0:0.529569:0.0:-0.0436874 +10 32560564 1KG_10_32560564 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.409735:0.0:0.0459244 +10 33123774 1KG_10_33123774 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.937353:0.0:-0.0140285 10 38343680 newrs148335528 G T . PASS . GT:GQ:BAF:LRR 0/0:0.467283:0.0:0.0467212 10 43615577 newrs146838520 C T . PASS . GT:GQ:BAF:LRR 0/0:0.490596:0.0:0.0395851 +10 43971618 1KG_10_43971618 T TA . PASS . GT:GQ:BAF:LRR 0/0:0.510112:0.0:-0.040054 10 50916603 newrs148244498 G A . PASS . GT:GQ:BAF:LRR 0/0:0.517626:0.0:-0.456432 10 63957819 newrs147070919 G A . PASS . GT:GQ:BAF:LRR 0/0:0.518923:0.0:-0.0639654 10 64414691 newrs149781580 G A . PASS . GT:GQ:BAF:LRR 0/0:0.400712:0.00579476356506:0.0207258 +10 64952698 1KG_10_64952698 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.484963:0.00261646509171:-0.0852815 +10 70174807 1KG_10_70174807 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.513087:0.0:0.129015 +10 70253255 1KG_10_70253255 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.409228:0.0:-0.195552 +10 72434641 1KG_10_72434641 G GAGGATTTTC . PASS . GT:GQ:BAF:LRR 0/0:0.499902:0.0:-0.963942 10 73082714 newrs148956476 G A . PASS . GT:GQ:BAF:LRR 0/0:0.499416:0.0:-0.4076 +10 73500627 1KG_10_73500627 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.496431:0.0277485251427:-0.299923 10 75542124 newrs150644371 G A . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:-0.0799351 10 79760832 newrs146957784 G A . PASS . GT:GQ:BAF:LRR 0/0:0.477549:0.0:0.0317019 10 82185762 newrs150786234 G A . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:0.0422308 10 85982437 newrs149695318 C A . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0100020766258:0.0359495 10 90428514 newrs147791767 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519044:0.0:-0.168957 +10 90974667 1KG_10_90974667 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.415577:0.0155762:-0.478504 +10 91198498 1KG_10_91198498 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.00940562 10 92635313 newrs149794455 A G . PASS . GT:GQ:BAF:LRR 0/0:0.499538:0.00889996:-0.571601 +10 94774024 1KG_10_94774024 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.499875:0.0:-0.627082 +10 95115488 1KG_10_95115488 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.414345:0.0:-0.117879 10 95262876 newrs146596670 C T . PASS . GT:GQ:BAF:LRR 0/0:0.336205:0.0:0.0788771 +10 96796973 1KG_10_96796973 T TCAA . PASS . GT:GQ:BAF:LRR 0/0:0.511852:0.0:0.0843414 10 96824564 newrs146962089 C T . PASS . GT:GQ:BAF:LRR 0/0:0.480633:0.0:0.137482 +10 98182460 1KG_10_98182460 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.312218:0.0:0.025126 10 98924593 newrs149092674 G T . PASS . GT:GQ:BAF:LRR 0/0:0.476294:0.0:-0.0925921 +10 99219883 1KG_10_99219883 T TCGGCATGGC . PASS . GT:GQ:BAF:LRR 0/0:0.330651:0.0:0.154153 +10 99968659 1KG_10_99968659 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.321781:0.0:-0.0411113 10 100017402 newrs150271620 C T . PASS . GT:GQ:BAF:LRR 0/0:0.501296:0.0:-0.14171 10 101460763 newrs147079897 C T . PASS . GT:GQ:BAF:LRR 0/0:0.440935:0.0:0.0516604 10 101462431 newrs149232042 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.238669 +10 101715768 1KG_10_101715768 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.376958:0.0257361531258:0.0512976 10 102013179 newrs150239404 G A . PASS . GT:GQ:BAF:LRR 0/0:0.476607:0.0:0.0762578 +10 102265185 1KG_10_102265185 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.4168:0.0730514:-0.947617 +10 102584498 1KG_10_102584498 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.426687:0.0:0.103501 10 105780318 newrs147985366 C T . PASS . GT:GQ:BAF:LRR 0/0:0.514751:0.0:-0.165547 +10 105796247 1KG_10_105796247 T TA . PASS . GT:GQ:BAF:LRR 0/0:0.501788:0.0:-0.0112749 10 105832966 newrs147734242 A C . PASS . GT:GQ:BAF:LRR 0/0:0.351044:0.00517626:0.0590782 10 106159259 newrs150734798 G A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0238655805588:-0.0082339 10 114182199 newrs149581330 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.0646247 +10 115662307 1KG_10_115662307 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.496237:0.0:-0.0399661 10 120920436 newrs147648163 G A . PASS . GT:GQ:BAF:LRR 0/0:0.515544:0.0193114280701:-0.0458524 +10 122664155 1KG_10_122664155 T TAGAC . PASS . GT:GQ:BAF:LRR 0/0:0.462962:0.0:-0.0697372 10 124708272 newrs147972795 C T . PASS . GT:GQ:BAF:LRR 0/0:0.884711:0.0:-0.0281962 10 126453960 newrs147429177 C T . PASS . GT:GQ:BAF:LRR 0/0:0.514392:0.0:0.123145 +10 126715803 1KG_10_126715803 C CCT . PASS . GT:GQ:BAF:LRR 0/0:0.498676:0.0:-0.521852 +10 127451949 1KG_10_127451949 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.333344:0.0697536:-1.43876 10 127456101 newrs146637402 A G . PASS . GT:GQ:BAF:LRR 0/0:0.495607:0.0:0.03097 10 127519995 newrs147798836 C T . PASS . GT:GQ:BAF:LRR 0/0:0.495904:0.0:0.0649443 +10 129901545 1KG_10_129901545 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.402314:0.0:0.0535203 +10 134885480 1KG_10_134885480 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.491374:0.0:0.285297 +10 135026424 1KG_10_135026424 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.84105:0.0:0.187366 +11 500597 1KG_11_500597 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.483299:0.0:0.220295 11 1092350 newrs146769199 G T . PASS . GT:GQ:BAF:LRR 0/0:0.464376:0.0:0.137696 11 3845507 newrs147354096 C T . PASS . GT:GQ:BAF:LRR 0/0:0.504719:0.004449903965:-0.256221 +11 4566459 1KG_11_4566459 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.463835:0.0154430866241:-0.189298 +11 4903673 1KG_11_4903673 T TACCACCCC . PASS . GT:GQ:BAF:LRR 0/0:0.712879:0.0:-0.00718887 +11 5173321 1KG_11_5173321 T TTCAGGCAC . PASS . GT:GQ:BAF:LRR 0/0:0.446922:0.0:-0.0778164 +11 5529917 1KG_11_5529917 C CTGG . PASS . GT:GQ:BAF:LRR 0/0:0.210233:0.0:-0.227464 +11 5566354 1KG_11_5566354 T TA . PASS . GT:GQ:BAF:LRR 0/0:0.406466:0.00101137161255:0.0580213 +11 5632154 1KG_11_5632154 T TCTC . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:-0.00264408 11 5686886 newrs150799809 C T . PASS . GT:GQ:BAF:LRR 0/0:0.511202:0.0:0.04264 +11 5699498 1KG_11_5699498 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.0182406 +11 5809806 1KG_11_5809806 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.39409:0.0:0.101252 11 6129810 newrs150485733 C T . PASS . GT:GQ:BAF:LRR 0/0:0.41881:0.0:0.264216 +11 6173684 1KG_11_6173684 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.441196:0.0:0.129335 11 6220736 newrs149905780 C T . PASS . GT:GQ:BAF:LRR 0/0:0.517395:0.000857532024384:-0.273309 +11 6231502 1KG_11_6231502 C CTT . PASS . GT:GQ:BAF:LRR 0/0:0.490721:0.00302934646606:-0.539058 11 6262908 newrs150327554 C T . PASS . GT:GQ:BAF:LRR 0/0:0.426473:0.0:0.121701 +11 6524023 1KG_11_6524023 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.497239:0.0:-0.0323305 +11 6816483 1KG_11_6816483 A AGCCAGCAGCC . PASS . GT:GQ:BAF:LRR 0/0:0.376958:0.0:-0.15648 11 6913227 newrs148113613 G A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.0696338 11 7672131 newrs149262617 C T . PASS . GT:GQ:BAF:LRR 0/0:0.473034:0.0359147787094:-0.104774 11 7949333 newrs147185885 G A . PASS . GT:GQ:BAF:LRR 0/0:0.421756:0.0:-0.0509975 +11 7981283 1KG_11_7981283 C CCTT . PASS . GT:GQ:BAF:LRR 0/0:0.514785:0.0:-0.0549284 +11 7981705 1KG_11_7981705 C CTTTGGT . PASS . GT:GQ:BAF:LRR 0/0:0.508516:0.0:0.044233 11 8120422 newrs147394931 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.112725 +11 8959232 1KG_11_8959232 G GTT . PASS . GT:GQ:BAF:LRR 0/0:0.892719:0.0:-0.00815356 +11 9304991 1KG_11_9304991 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.462691:0.0:-0.405376 +11 10516495 1KG_11_10516495 C CTG . PASS . GT:GQ:BAF:LRR 0/0:0.483115:0.0:-0.0548522 11 10518408 newrs147243781 G T . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.00283265113831:-0.0167666 11 10555597 newrs149870408 C A . PASS . GT:GQ:BAF:LRR 0/0:0.511667:0.000948667526245:-0.185732 11 10585814 newrs149004349 C A . PASS . GT:GQ:BAF:LRR 0/0:0.510589:0.0:-0.0579392 +11 12518086 1KG_11_12518086 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.480417:0.0:-0.224026 +11 14901998 1KG_11_14901998 C CAAG . PASS . GT:GQ:BAF:LRR 0/0:0.507982:0.0:-0.159648 11 16424346 newrs147886976 C T . PASS . GT:GQ:BAF:LRR 0/0:0.509721:0.0:0.0419625 +11 17417216 1KG_11_17417216 G GGT . PASS . GT:GQ:BAF:LRR 0/0:0.396652:0.00352549552917:0.108287 11 17542960 newrs147956944 T G . PASS . GT:GQ:BAF:LRR 0/0:0.404434:0.0:-0.16419 +11 18327766 1KG_11_18327766 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.438792:0.0:0.0795359 +11 18451402 1KG_11_18451402 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:0.0157807 +11 18478278 1KG_11_18478278 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.446544:0.0:0.027349 +11 18500367 1KG_11_18500367 C CAA . PASS . GT:GQ:BAF:LRR 0/0:0.503235:0.0:0.0434554 +11 18553941 1KG_11_18553941 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.498582:0.0107446908951:0.00529816 11 19077207 newrs150168108 C T . PASS . GT:GQ:BAF:LRR 0/0:0.495872:0.0:0.139944 +11 19174200 1KG_11_19174200 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.514191:0.0:0.185837 11 19246240 newrs150255844 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.507128 +11 26587349 1KG_11_26587349 C CG . PASS . GT:GQ:BAF:LRR 0/0:0.346175:0.0:0.142197 +11 26621211 1KG_11_26621211 T TCTG . PASS . GT:GQ:BAF:LRR 0/0:0.483192:0.0:-0.351535 11 30937137 newrs150388476 G A . PASS . GT:GQ:BAF:LRR 0/0:0.49798:0.0:0.0827253 +11 32611187 1KG_11_32611187 G GTGAT . PASS . GT:GQ:BAF:LRR 0/0:0.901018:0.0:0.0208276 +11 33054901 1KG_11_33054901 T TTGA . PASS . GT:GQ:BAF:LRR 0/0:0.501102:0.0:0.289147 +11 33374949 1KG_11_33374949 T TCAC . PASS . GT:GQ:BAF:LRR 0/0:0.410511:0.0:0.142907 +11 33605028 1KG_11_33605028 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.502816:0.0:-0.162042 11 34165021 newrs148378865 G A . PASS . GT:GQ:BAF:LRR 0/0:0.506558:0.0:0.100185 +11 34654157 1KG_11_34654157 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.797503:0.0:-0.0941642 11 34979130 newrs148117169 G A . PASS . GT:GQ:BAF:LRR 0/0:0.443788:0.0:0.13915 +11 36614525 1KG_11_36614525 T TTCA . PASS . GT:GQ:BAF:LRR 0/0:0.511852:0.00867462158203:0.0222608 +11 45928418 1KG_11_45928418 A ACCAT . PASS . GT:GQ:BAF:LRR 0/0:0.498639:0.0:0.0237494 +11 46776446 1KG_11_46776446 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.47258:0.0:-0.0660011 11 47298298 newrs147179561 C T . PASS . GT:GQ:BAF:LRR 0/0:0.442723:0.00542795658112:0.00624628 +11 47436693 1KG_11_47436693 G GGAA . PASS . GT:GQ:BAF:LRR 0/0:0.448196:0.0:0.116728 11 47690393 newrs150818119 C T . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.00559258460999:-0.00667744 +11 47731971 1KG_11_47731971 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.511852:0.0:-0.00284671 +11 50003377 1KG_11_50003377 T TCA . PASS . GT:GQ:BAF:LRR 0/0:0.523305:0.0:-0.0318557 11 55339895 newrs149911886 C T . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.0:-0.0346859 +11 55594979 1KG_11_55594979 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.00546091:0.172566 +11 55606810 newrs147515254 TATCTC T . PASS . GT:GQ:BAF:LRR 0/0:0.781395:0.0:0.0424 +11 56949678 1KG_11_56949678 C CAGA . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:0.0301318 +11 57106032 1KG_11_57106032 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.500145:0.0:-0.0912961 11 57148121 newrs149309930 C T . PASS . GT:GQ:BAF:LRR 0/0:0.451699:0.0:-0.0227875 +11 57982424 1KG_11_57982424 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.336045:0.0:0.200866 11 58491889 newrs150657394 C T . PASS . GT:GQ:BAF:LRR 0/0:0.499688:0.0:-0.11501 +11 59224767 1KG_11_59224767 A AT . PASS . GT:GQ:BAF:LRR 0/0:0.501845:0.0:-1.73866 11 59224880 newrs146734452 G A . PASS . GT:GQ:BAF:LRR ./.:0.0677895:0.0205971002579:-1.62045 +11 59271099 1KG_11_59271099 T TACTC . PASS . GT:GQ:BAF:LRR 0/0:0.517351:0.0:-0.135031 +11 59609989 1KG_11_59609989 G GTTC . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:-0.067991 +11 59631466 1KG_11_59631466 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.379341:0.0:0.00836143 11 59810966 newrs149225217 G A . PASS . GT:GQ:BAF:LRR 0/0:0.511847:0.0:0.0935151 11 60183438 newrs150784858 C T . PASS . GT:GQ:BAF:LRR 0/0:0.374745:0.0104249119759:0.0299738 11 60268634 newrs150012278 C A . PASS . GT:GQ:BAF:LRR 0/0:0.517754:0.0:-0.235949 +11 61205520 1KG_11_61205520 T TA . PASS . GT:GQ:BAF:LRR 0/0:0.517748:0.00304710865021:-0.0791702 +11 62490079 1KG_11_62490079 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.380533:0.0:0.0409432 11 62502922 newrs150104999 C T . PASS . GT:GQ:BAF:LRR 0/0:0.513799:0.0:-0.0566828 11 62652683 newrs147281603 C T . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.0:0.0194589 +11 63486517 1KG_11_63486517 T TAA . PASS . GT:GQ:BAF:LRR 0/0:0.511727:0.0:0.153104 11 64004657 newrs147883767 A G . PASS . GT:GQ:BAF:LRR 0/0:0.39033:0.0086501:-0.292782 +11 64011496 1KG_11_64011496 C CTG . PASS . GT:GQ:BAF:LRR 0/0:0.499605:0.0:0.0840626 +11 64815818 1KG_11_64815818 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.480417:0.0:0.110551 +11 70118468 1KG_11_70118468 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.480417:0.0:0.0269111 +11 70279816 1KG_11_70279816 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.160235:0.104746:-0.0595635 +11 71806541 1KG_11_71806541 C CCTGGA . PASS . GT:GQ:BAF:LRR 0/0:0.498771:0.0:-0.111041 11 73610190 newrs147312150 G A . PASS . GT:GQ:BAF:LRR 0/0:0.489787:0.0203649997711:-0.0325025 +11 73638355 1KG_11_73638355 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.485584:0.0254566:-0.260198 +11 77383240 1KG_11_77383240 C CAAAATCATCACT . PASS . GT:GQ:BAF:LRR 0/0:0.507862:0.0:0.319124 +11 78279775 1KG_11_78279775 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.429791:0.0:-0.0396729 11 82625793 newrs147443808 C T . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.0118647 +11 82644887 1KG_11_82644887 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.851266:0.0:0.0875176 11 82947475 newrs150299461 C T . PASS . GT:GQ:BAF:LRR 0/0:0.511187:0.0:-0.201803 11 85444980 newrs146718885 A G . PASS . GT:GQ:BAF:LRR 0/0:0.489319:0.0:-0.246762 11 86108785 newrs150754388 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.108652 @@ -668,244 +1260,549 @@ 11 88911706 newrs147574809 G A . PASS . GT:GQ:BAF:LRR 0/0:0.516684:0.0:-0.237684 11 88961060 newrs149912348 A G . PASS . GT:GQ:BAF:LRR 0/0:0.529569:0.0:0.0785688 11 94134180 newrs148986490 G T . PASS . GT:GQ:BAF:LRR 0/0:0.435487:0.00298118591309:0.00131885 +11 94189472 1KG_11_94189472 A AT . PASS . GT:GQ:BAF:LRR 0/0:0.514785:0.015814602375:-0.404921 +11 94862348 1KG_11_94862348 A AATGGCATAGAAAGTTGCCTTT . PASS . GT:GQ:BAF:LRR 0/0:0.461178:0.0188332796097:-0.654517 +11 96124151 1KG_11_96124151 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.041516 11 102562717 newrs149812545 G T . PASS . GT:GQ:BAF:LRR 0/0:0.491768:0.0:0.148066 11 102573704 newrs148894063 G A . PASS . GT:GQ:BAF:LRR 0/0:0.429207:0.0:0.0653236 +11 103124075 1KG_11_103124075 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.517255:0.0:0.206186 +11 104879686 1KG_11_104879686 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.475742:0.0:0.176432 11 104916018 newrs150516068 C T . PASS . GT:GQ:BAF:LRR 0/0:0.40302:0.0:-0.168883 +11 105804655 1KG_11_105804655 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.365495:0.0:-0.0915945 11 108158399 newrs147600485 A G . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.308222 11 108332229 newrs149955947 G A . PASS . GT:GQ:BAF:LRR 0/0:0.502425:0.0:0.119168 11 108381145 newrs149024755 G A . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:0.121641 11 111888614 newrs150406695 A G . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:0.0611805 +11 111953288 1KG_11_111953288 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.472485:0.0:0.056854 11 112104210 newrs150726932 G T . PASS . GT:GQ:BAF:LRR 0/0:0.510946:0.0:0.127193 +11 113567640 1KG_11_113567640 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.47067:0.0:0.000146522 11 113614519 newrs150184757 C T . PASS . GT:GQ:BAF:LRR 0/0:0.864861:0.0:0.110055 +11 113853842 1KG_11_113853842 C CG . PASS . GT:GQ:BAF:LRR 0/0:0.353328:0.00103412:-1.07281 +11 118374245 1KG_11_118374245 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.425585:0.0:0.0224564 11 118531332 newrs147240748 G A . PASS . GT:GQ:BAF:LRR 0/0:0.495879:0.0:-0.0928038 11 119042182 newrs148683955 G A . PASS . GT:GQ:BAF:LRR 0/0:0.451091:0.0:-0.208553 11 119167745 newrs148996708 G A . PASS . GT:GQ:BAF:LRR 0/0:0.483076:0.0399552583694:-0.222996 +11 121393322 1KG_11_121393322 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.285956:0.0:-0.764592 +11 123755982 1KG_11_123755982 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.398255:0.0:0.0924076 +11 123994135 1KG_11_123994135 T TGG . PASS . GT:GQ:BAF:LRR 0/0:0.418711:0.0:-0.163717 +11 124495753 1KG_11_124495753 T TAAG . PASS . GT:GQ:BAF:LRR 0/0:0.49281:0.0:0.194359 11 124496808 newrs149295558 C T . PASS . GT:GQ:BAF:LRR 0/0:0.499712:0.0:-0.052869 +11 124509660 1KG_11_124509660 T TTGGGCATCTTTGGG . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.000269364:0.0203118 +11 124745539 1KG_11_124745539 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.400819:0.00178686:-0.198316 11 124761459 newrs147387634 C T . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.0475243 +11 124861410 1KG_11_124861410 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.511769:0.0:0.132308 11 125766086 newrs147862544 G A . PASS . GT:GQ:BAF:LRR 0/0:0.336045:0.0091450214386:0.121075 +11 125795378 1KG_11_125795378 A AT . PASS . GT:GQ:BAF:LRR 0/0:0.511385:0.00476098060608:-0.616121 11 125864808 newrs149220812 G T . PASS . GT:GQ:BAF:LRR 0/0:0.511512:0.000152826309204:0.118508 +11 130343253 1KG_11_130343253 C CCTT . PASS . GT:GQ:BAF:LRR 0/0:0.512889:0.0:0.0342344 +11 130716061 1KG_11_130716061 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.474367:0.0:0.0427795 11 133715087 newrs150527694 T G . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:0.000637571 11 134010629 newrs146878298 C T . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.0309197 11 134121125 newrs149874205 G A . PASS . GT:GQ:BAF:LRR 0/0:0.517529:0.0:0.0266778 +11 134158762 1KG_11_134158762 C CAT . PASS . GT:GQ:BAF:LRR 0/0:0.50944:0.0:0.238172 +11 134183862 1KG_11_134183862 A ACT . PASS . GT:GQ:BAF:LRR 0/0:0.513685:0.0:0.11883 12 547528 newrs149946039 T G . PASS . GT:GQ:BAF:LRR 0/0:0.526609:0.0:-0.125997 +12 1023658 1KG_12_1023658 T TA . PASS . GT:GQ:BAF:LRR 0/0:0.885115:0.0:0.14807 +12 2968456 1KG_12_2968456 T TTTCTCCGAGACCGGC . PASS . GT:GQ:BAF:LRR 0/0:0.482886:0.0:-0.460531 +12 2974538 1KG_12_2974538 G GCAATTGTGGAGACCCTGGGTC . PASS . GT:GQ:BAF:LRR 0/0:0.408735:0.00324016809464:0.0510987 +12 3747324 1KG_12_3747324 C CG . PASS . GT:GQ:BAF:LRR 0/0:0.410847:0.0132988:0.00842332 +12 3782644 1KG_12_3782644 C CTCATGGGCT . PASS . GT:GQ:BAF:LRR 0/0:0.410447:0.0:0.113699 12 6182789 newrs147924974 G T . PASS . GT:GQ:BAF:LRR 0/0:0.348259:0.0:0.121485 12 6631204 newrs149296057 G A . PASS . GT:GQ:BAF:LRR 0/0:0.517516:0.0:0.18005 +12 6924041 1KG_12_6924041 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.511852:0.0:0.0069915 +12 6925338 1KG_12_6925338 G GCGGAGA . PASS . GT:GQ:BAF:LRR 0/0:0.477769:0.0114661455154:-0.368316 12 7043191 newrs147637415 G A . PASS . GT:GQ:BAF:LRR 0/0:0.517448:0.0:0.220633 +12 7244125 1KG_12_7244125 T TGG . PASS . GT:GQ:BAF:LRR 0/0:0.429814:0.0:0.209422 +12 7973860 1KG_12_7973860 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.470998:0.0:0.00761983 12 8212133 newrs149088151 G A . PASS . GT:GQ:BAF:LRR 0/0:0.434579:0.0:0.0347664 12 9318694 newrs150067154 G A . PASS . GT:GQ:BAF:LRR 0/0:0.511852:0.0:0.0547247 12 9353641 newrs147359935 G A . PASS . GT:GQ:BAF:LRR 0/0:0.494992:0.00515085458755:-0.42624 12 10167887 newrs148805742 G A . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:0.0744616 +12 11091072 1KG_12_11091072 C CAG . PASS . GT:GQ:BAF:LRR 0/0:0.514655:0.0:0.124426 12 11138813 newrs146930737 G T . PASS . GT:GQ:BAF:LRR 0/0:0.444634:0.0:-0.0895737 12 11175056 newrs146593308 G A . PASS . GT:GQ:BAF:LRR 0/0:0.517591:0.0:0.132098 12 11507474 newrs149040356 C A . PASS . GT:GQ:BAF:LRR 0/0:0.495418:0.0:-0.514673 +12 12315260 1KG_12_12315260 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.493391:0.0:-0.0558378 +12 12974190 1KG_12_12974190 C CCTTTG . PASS . GT:GQ:BAF:LRR 0/0:0.511681:0.0038058757782:-0.971663 12 13220190 newrs148941252 C T . PASS . GT:GQ:BAF:LRR 0/0:0.492975:0.0:-0.221685 +12 13238154 1KG_12_13238154 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.336045:0.00155091285706:0.0330645 +12 13716360 1KG_12_13716360 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:-0.161805 +12 14689561 1KG_12_14689561 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.494574:0.0:-0.00496231 12 15679198 newrs150178443 T C . PASS . GT:GQ:BAF:LRR 0/0:0.491291:0.0:-0.0348158 +12 18691183 1KG_12_18691183 T TTGCTGTCG . PASS . GT:GQ:BAF:LRR 0/0:0.450201:0.0:-0.350032 +12 18852853 1KG_12_18852853 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.472741:0.00857669115067:-0.326862 12 21799831 newrs149479698 A G . PASS . GT:GQ:BAF:LRR 0/0:0.499838:0.0:-0.391543 +12 22677475 1KG_12_22677475 A AT . PASS . GT:GQ:BAF:LRR 0/0:0.499202:0.0:-0.141478 +12 22796931 1KG_12_22796931 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.501438:0.0:0.275841 12 25679747 newrs150558545 G A . PASS . GT:GQ:BAF:LRR 0/0:0.498379:0.0:0.133149 12 29460778 newrs148185891 C A . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:-0.0190527 +12 29469893 1KG_12_29469893 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.462962:0.0:-0.401478 +12 29604299 1KG_12_29604299 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.460167:0.000378549098969:-0.0199907 12 30790063 newrs148376849 G A . PASS . GT:GQ:BAF:LRR 0/0:0.415368:0.0:-0.0387285 12 30864505 newrs150085536 G A . PASS . GT:GQ:BAF:LRR 0/0:0.403649:0.0:-0.186096 12 32138688 newrs147453939 T G . PASS . GT:GQ:BAF:LRR 0/0:0.436548:0.0:-0.189563 +12 32906956 1KG_12_32906956 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.51039:0.00161969661713:0.0551167 12 40001518 newrs147085772 T G . PASS . GT:GQ:BAF:LRR 0/0:0.500162:0.0:-0.219847 12 40653379 newrs150368439 C T . PASS . GT:GQ:BAF:LRR 0/0:0.498608:0.0:-0.114147 12 41421776 newrs148453314 A G . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:0.0264907 12 48110672 newrs150299683 C T . PASS . GT:GQ:BAF:LRR 0/0:0.49919:0.0:0.0169383 12 49255792 newrs147876425 C T . PASS . GT:GQ:BAF:LRR 0/0:0.897003:0.0:-0.295595 +12 49314780 1KG_12_49314780 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.499294:0.00448679924011:0.0639389 12 49460259 newrs148047837 C T . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.0:0.121282 +12 51089120 1KG_12_51089120 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.466036:0.0113114:-0.292719 12 51393026 newrs150400273 T C . PASS . GT:GQ:BAF:LRR 0/0:0.458406:0.00810786:-1.05378 +12 52188385 1KG_12_52188385 G GAACATCTTC . PASS . GT:GQ:BAF:LRR 0/0:0.391304:0.0:-0.0319944 +12 52201212 1KG_12_52201212 A AGAG . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.170193 +12 52470928 1KG_12_52470928 T TCAC . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.152107 12 52912732 newrs147185753 G A . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.00681835412979:-0.177377 +12 53553435 1KG_12_53553435 C CTCTCCTGCT . PASS . GT:GQ:BAF:LRR 0/0:0.400248:0.0:-0.142211 +12 53702123 1KG_12_53702123 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.510977:0.000254988670349:-0.0456061 +12 55356700 1KG_12_55356700 G GCTT . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.0786186 +12 56080059 1KG_12_56080059 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.863858:0.0644645690918:-0.69642 12 56522494 newrs147784540 G T . PASS . GT:GQ:BAF:LRR 0/0:0.412205:0.0:-0.193535 +12 56631124 1KG_12_56631124 GGTGA G . PASS . GT:GQ:BAF:LRR 0/0:0.396584:0.0:-0.232032 12 56817237 newrs149262573 G A . PASS . GT:GQ:BAF:LRR 0/0:0.376958:0.00743329524994:-0.166376 12 56868326 newrs146654208 A G . PASS . GT:GQ:BAF:LRR 0/0:0.500032:0.0:0.0307203 12 56975233 newrs146998541 C T . PASS . GT:GQ:BAF:LRR 0/0:0.351044:0.0:-0.0827936 +12 57407436 1KG_12_57407436 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.173525:0.13505:-0.00710487 12 57431332 newrs149628462 A G . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:-0.0208024 +12 57435214 1KG_12_57435214 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.506848:0.0:-0.204885 12 57454555 newrs149540426 C T . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.226693 +12 57629571 1KG_12_57629571 CG C . PASS . GT:GQ:BAF:LRR 0/0:0.448533:0.0:-0.213142 +12 57908612 1KG_12_57908612 C CACCAGCT . PASS . GT:GQ:BAF:LRR 0/0:0.511852:0.000651597976685:0.0554316 +12 58016602 1KG_12_58016602 A AGCTGCCCAGGATTCTG . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.0:-0.161299 +12 63225931 1KG_12_63225931 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.511248:0.0:-0.247336 +12 66605332 1KG_12_66605332 A AGT . PASS . GT:GQ:BAF:LRR 0/0:0.496453:0.0:-0.00155866 +12 67705503 1KG_12_67705503 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.480417:0.0:0.142672 +12 70072630 1KG_12_70072630 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.493936:0.012523829937:0.141186 +12 70824404 1KG_12_70824404 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.482039:0.0:-0.175143 12 71533491 newrs146656002 C A . PASS . GT:GQ:BAF:LRR 0/0:0.486986:0.00406295061111:-0.0547003 +12 72091064 1KG_12_72091064 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.467283:0.0:-0.00649197 +12 75728526 1KG_12_75728526 A ATTCAG . PASS . GT:GQ:BAF:LRR 0/0:0.512876:0.0:-0.708509 +12 80865911 1KG_12_80865911 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.514087:0.0:-0.0905537 +12 83290132 1KG_12_83290132 C CTT . PASS . GT:GQ:BAF:LRR 0/0:0.473749:0.0:0.148776 12 85255518 newrs146589974 G A . PASS . GT:GQ:BAF:LRR 0/0:0.493611:0.0:-0.352324 12 85515611 newrs148400374 C T . PASS . GT:GQ:BAF:LRR 0/0:0.509903:0.0:0.121781 12 89814944 newrs148916260 G A . PASS . GT:GQ:BAF:LRR 0/0:0.511852:0.0:-0.49853 12 93139253 newrs149205825 G A . PASS . GT:GQ:BAF:LRR 0/0:0.418933:0.0:-0.0995775 +12 95445702 1KG_12_95445702 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.409169:0.0:-0.00479518 +12 96288785 1KG_12_96288785 G GGAT . PASS . GT:GQ:BAF:LRR 0/0:0.507787:0.0:-0.165374 12 96386479 newrs149004222 G A . PASS . GT:GQ:BAF:LRR 0/0:0.493798:0.0:-0.0689596 +12 98921671 1KG_12_98921671 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.483371:0.000508189201355:-0.669357 +12 99071206 1KG_12_99071206 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.50719:0.0:-0.410948 +12 101133726 1KG_12_101133726 C CTT . PASS . GT:GQ:BAF:LRR ./.:0.056436:0.0997822284698:-0.252226 +12 101473039 1KG_12_101473039 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.37207:0.0:-0.0232736 12 101577912 newrs149078919 C T . PASS . GT:GQ:BAF:LRR 0/0:0.515374:0.0:-0.0211334 +12 101679384 1KG_12_101679384 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.476743:0.0:-0.18758 12 102131005 newrs149836328 G A . PASS . GT:GQ:BAF:LRR 0/0:0.499902:0.0:-0.300278 12 102437878 newrs147510623 C T . PASS . GT:GQ:BAF:LRR 0/0:0.50465:0.0:0.226673 +12 102492922 1KG_12_102492922 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.464045:0.00333109:-0.442081 12 103288566 newrs148393887 T C . PASS . GT:GQ:BAF:LRR 0/0:0.516955:0.0:-0.215266 12 104031811 newrs149696858 C T . PASS . GT:GQ:BAF:LRR 0/0:0.396067:0.0146797895432:-0.0488444 12 104378575 newrs149399146 C T . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.0:0.0222286 12 106804655 newrs148879912 C T . PASS . GT:GQ:BAF:LRR 0/0:0.510047:0.0:-0.36265 +12 107937795 1KG_12_107937795 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.022661447525:0.0648255 +12 107974767 1KG_12_107974767 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.493151:0.0123884677887:-0.15941 +12 108939095 1KG_12_108939095 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.371617:0.0:0.112302 +12 110950598 1KG_12_110950598 C CATAAT . PASS . GT:GQ:BAF:LRR 0/0:0.502244:0.00171446800232:0.0886191 +12 110969388 1KG_12_110969388 G GGAAA . PASS . GT:GQ:BAF:LRR 0/0:0.524239:0.0:-0.902057 +12 111317841 1KG_12_111317841 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.500191:0.0:-0.394883 +12 111885815 1KG_12_111885815 C CTCCCTTCCTCACTGGGATTCAGAG . PASS . GT:GQ:BAF:LRR 0/0:0.358249:0.00915145874023:-0.0122097 +12 112590265 1KG_12_112590265 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.0:0.00921048 +12 112846124 1KG_12_112846124 C CCTT . PASS . GT:GQ:BAF:LRR 0/0:0.515946:0.0:0.0446896 12 112940006 newrs148176616 C T . PASS . GT:GQ:BAF:LRR 0/0:0.204639:0.0:0.103787 12 113645335 newrs147913046 G A . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:-0.0160547 +12 114352777 1KG_12_114352777 A AAGAGCTCTC . PASS . GT:GQ:BAF:LRR 0/0:0.831291:0.0:0.0134789 12 114804165 newrs147405081 C T . PASS . GT:GQ:BAF:LRR 0/0:0.517404:0.0:-0.0578861 +12 117462111 1KG_12_117462111 G GGAGGT . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:-0.018207 +12 118520043 1KG_12_118520043 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.509124:0.0140962:-0.770112 12 121008995 newrs150629669 C A . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:0.0051172 12 121471459 newrs148845781 C A . PASS . GT:GQ:BAF:LRR 0/0:0.431302:0.0:0.107072 12 121613282 newrs149116962 G A . PASS . GT:GQ:BAF:LRR 0/0:0.376179:0.0:0.0550921 12 121687764 newrs147402468 T C . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.0:0.135268 +12 122281716 1KG_12_122281716 C CCT . PASS . GT:GQ:BAF:LRR 0/0:0.498041:0.000812172889709:0.00917237 +12 122295273 1KG_12_122295273 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.467283:0.0283384:-0.453859 +12 123019273 1KG_12_123019273 C CCAAT . PASS . GT:GQ:BAF:LRR 0/0:0.515546:0.0:0.112413 +12 123265759 1KG_12_123265759 T TAAA . PASS . GT:GQ:BAF:LRR 0/0:0.510441:0.0:0.135207 +12 123307940 1KG_12_123307940 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.514717:0.0:-0.214554 +12 123435007 1KG_12_123435007 G GCCA . PASS . GT:GQ:BAF:LRR 0/0:0.508277:0.0:-0.341544 12 124097800 newrs149103406 G T . PASS . GT:GQ:BAF:LRR 0/0:0.515712:0.0:-0.000184893 12 124114714 newrs148513104 A C . PASS . GT:GQ:BAF:LRR 0/0:0.334046:0.0115446:-0.706299 +12 124158228 1KG_12_124158228 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.51165:0.0:-0.432752 12 124210832 newrs147005791 G A . PASS . GT:GQ:BAF:LRR 0/0:0.476306:0.00199675559998:0.133518 +12 132281733 1KG_12_132281733 G GAGA . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.00576400756836:0.141427 +12 132636859 1KG_12_132636859 C CG . PASS . GT:GQ:BAF:LRR 0/0:0.487384:0.0:0.0695265 +12 132688136 1KG_12_132688136 C CATA . PASS . GT:GQ:BAF:LRR 0/0:0.498122:0.0:-1.22342 12 133438222 newrs148932455 T C . PASS . GT:GQ:BAF:LRR 0/0:0.371867:0.00143908:0.123477 +12 133698495 1KG_12_133698495 T TA . PASS . GT:GQ:BAF:LRR 0/0:0.496209:0.0:0.035967 13 19752385 newrs148979711 C T . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:0.113743 +13 25444834 1KG_13_25444834 T TAAG . PASS . GT:GQ:BAF:LRR 0/0:0.493052:0.0:-0.0210524 13 25828033 newrs150032485 C T . PASS . GT:GQ:BAF:LRR 0/0:0.519034:0.00173681974411:0.0327747 +13 31860865 1KG_13_31860865 G GGAAA . PASS . GT:GQ:BAF:LRR 0/0:0.513508:0.0:-1.23831 +13 32913733 1KG_13_32913733 C CTA . PASS . GT:GQ:BAF:LRR 0/0:0.901895:0.0:0.263255 +13 32929108 1KG_13_32929108 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.499708:0.0:-0.0568335 13 36748613 newrs148826039 C T . PASS . GT:GQ:BAF:LRR 0/0:0.403126:0.0:0.114596 13 37569125 newrs148564105 C A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.00277745723724:-0.0530646 +13 37598190 1KG_13_37598190 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.387908:0.0:0.12383 +13 37679380 1KG_13_37679380 C CTGT . PASS . GT:GQ:BAF:LRR 0/0:0.492803:0.0:-0.60874 +13 38153190 1KG_13_38153190 T TA . PASS . GT:GQ:BAF:LRR 0/0:0.512026:0.0:0.00119083 13 38171321 newrs149175978 G A . PASS . GT:GQ:BAF:LRR 0/0:0.871759:0.0:0.0379355 +13 42407540 1KG_13_42407540 C CG . PASS . GT:GQ:BAF:LRR 0/0:0.487962:0.052543:-0.645129 13 43500527 newrs149216994 G A . PASS . GT:GQ:BAF:LRR 0/0:0.499868:0.0:-0.0824176 13 43896520 newrs147465511 C T . PASS . GT:GQ:BAF:LRR 0/0:0.421506:0.0132063031197:-0.225517 13 45148546 newrs146993055 G A . PASS . GT:GQ:BAF:LRR 0/0:0.421133:0.0:0.0676405 +13 46701832 1KG_13_46701832 A ATT . PASS . GT:GQ:BAF:LRR 0/0:0.498827:0.0205979347229:-1.04732 13 50275987 newrs147153406 G T . PASS . GT:GQ:BAF:LRR 0/0:0.499631:0.0:0.0184289 +13 78173472 1KG_13_78173472 G GTC . PASS . GT:GQ:BAF:LRR 0/0:0.882385:0.0:-0.633519 13 94958377 newrs149343030 G A . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:0.11637 13 95838955 newrs149813736 C T . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:-0.251838 13 103525640 newrs147955525 A G . PASS . GT:GQ:BAF:LRR 0/0:0.519483:0.0:-0.290787 +13 110835577 1KG_13_110835577 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.416871:0.0:-0.258317 +13 111092149 1KG_13_111092149 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.483202:0.0:-0.167981 13 113053487 newrs146598083 G A . PASS . GT:GQ:BAF:LRR 0/0:0.500165:0.0:-0.000879787 13 113851339 newrs147592475 G T . PASS . GT:GQ:BAF:LRR 0/0:0.421849:0.0:0.222139 13 114154348 newrs147239381 C T . PASS . GT:GQ:BAF:LRR 0/0:0.501994:0.0:0.0145494 +14 20404319 1KG_14_20404319 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.333299:0.00895747:-0.142292 +14 20528600 newrs148115082 AG A . PASS . GT:GQ:BAF:LRR 0/0:0.865108:0.0:-0.997827 14 20848453 newrs150831074 C T . PASS . GT:GQ:BAF:LRR 0/0:0.419872:0.0:-0.669645 +14 20852013 1KG_14_20852013 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.454692:0.0:0.0745585 +14 21498756 1KG_14_21498756 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.379562:0.00395208597183:-1.47696 +14 21526398 1KG_14_21526398 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.842841:0.0:0.0143681 14 21623378 newrs149953865 G T . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.0:0.0936777 +14 22690212 newrs148538313 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.869905:0.0:-0.146227 14 23424338 newrs149965606 G A . PASS . GT:GQ:BAF:LRR 0/0:0.414767:0.0123677253723:0.0798318 14 23893116 newrs147727900 C T . PASS . GT:GQ:BAF:LRR 0/0:0.437842:0.0:0.0808325 14 24586536 newrs150144513 G A . PASS . GT:GQ:BAF:LRR 0/0:0.517166:0.0:0.0760514 +14 31355221 1KG_14_31355221 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.414695:0.0:0.0547939 +14 31582344 1KG_14_31582344 T TTGCTAG . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.0273124 +14 32562501 1KG_14_32562501 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.449554:0.0:-0.00502392 +14 35295293 1KG_14_35295293 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.501859:0.0:0.00827541 +14 36244844 1KG_14_36244844 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.398031:0.0:-0.841894 14 39543728 newrs148248798 C A . PASS . GT:GQ:BAF:LRR 0/0:0.500193:0.0:0.0514718 +14 45432176 1KG_14_45432176 A AGTT . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.014932513237:-0.108827 +14 45564695 1KG_14_45564695 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.512317:0.0195039:-0.405023 +14 51230579 1KG_14_51230579 A ACTT . PASS . GT:GQ:BAF:LRR 0/0:0.517816:0.0:0.0958857 14 51378470 newrs150547274 G T . PASS . GT:GQ:BAF:LRR 0/0:0.474113:0.0:0.120842 14 51381465 newrs150701003 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.00543302297592:-0.23124 +14 51446060 1KG_14_51446060 C CG . PASS . GT:GQ:BAF:LRR 0/0:0.227075:0.0208343:-0.88596 +14 51721134 1KG_14_51721134 C CAGA . PASS . GT:GQ:BAF:LRR 0/0:0.499159:0.0:0.169774 14 52741521 newrs150364594 C T . PASS . GT:GQ:BAF:LRR 0/0:0.511023:0.0:0.0707803 +14 55878530 1KG_14_55878530 G GGA . PASS . GT:GQ:BAF:LRR 0/0:0.398271:0.0283362269402:-0.753188 +14 57672624 1KG_14_57672624 A AGG . PASS . GT:GQ:BAF:LRR 0/0:0.473175:0.0:-0.0556078 +14 57710989 1KG_14_57710989 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.439042:0.0:-0.184448 +14 57948275 1KG_14_57948275 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.495609:0.0:-0.0154484 14 57949845 newrs149798976 G A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.00780492 +14 60611597 1KG_14_60611597 C CTT . PASS . GT:GQ:BAF:LRR 0/0:0.510146:0.0:-0.0560274 +14 60712633 1KG_14_60712633 A AAAG . PASS . GT:GQ:BAF:LRR 0/0:0.481688:0.0:-0.819869 +14 64065613 1KG_14_64065613 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.511852:0.0:0.0479523 14 64637040 newrs148965783 G T . PASS . GT:GQ:BAF:LRR 0/0:0.505974:0.0:0.00991983 14 64746697 newrs148022433 A G . PASS . GT:GQ:BAF:LRR 0/0:0.511232:0.0:0.0511489 14 65252552 newrs149186357 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.125513 14 67854084 newrs149261200 G A . PASS . GT:GQ:BAF:LRR 0/0:0.363299:0.0:-0.0932824 14 68934972 newrs148518198 G A . PASS . GT:GQ:BAF:LRR 0/0:0.515358:0.0:0.0268868 14 71522261 newrs149428100 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500204:0.0:-0.0479098 +14 72176329 1KG_14_72176329 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:-0.00279519 14 73421171 newrs149756917 G A . PASS . GT:GQ:BAF:LRR 0/0:0.497063:0.00985968112946:-0.450622 14 73614807 newrs149562759 G A . PASS . GT:GQ:BAF:LRR 0/0:0.505403:0.0:-0.0520427 +14 73716716 1KG_14_73716716 GC G . PASS . GT:GQ:BAF:LRR 0/0:0.503196:0.00251185894012:-0.203925 +14 73753835 1KG_14_73753835 A ATTT . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.109298 +14 74327298 1KG_14_74327298 G GATAAT . PASS . GT:GQ:BAF:LRR 0/0:0.506199:0.0:0.0133717 +14 74346768 1KG_14_74346768 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.33253:0.104242:-1.04776 14 74363143 newrs150263864 G A . PASS . GT:GQ:BAF:LRR 0/0:0.511695:0.006596326828:-0.5768 14 74443025 newrs149628087 A C . PASS . GT:GQ:BAF:LRR 0/0:0.352786:0.0200511:0.144456 +14 75265110 1KG_14_75265110 T TA . PASS . GT:GQ:BAF:LRR 0/0:0.401321:0.00261205434799:0.0698291 +14 75537785 1KG_14_75537785 C CGA . PASS . GT:GQ:BAF:LRR 0/0:0.491013:0.0:0.0283966 14 76186169 newrs147593414 G A . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:0.0495186 +14 76259418 1KG_14_76259418 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.467283:0.0:0.0770372 +14 76368485 1KG_14_76368485 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.79854:0.0410553:-0.451972 +14 77273057 1KG_14_77273057 C CTT . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:0.153005 14 77273847 newrs150078735 T G . PASS . GT:GQ:BAF:LRR 0/0:0.498132:0.0:0.000671952 14 77793851 newrs148051919 C T . PASS . GT:GQ:BAF:LRR 0/0:0.529202:0.0:-0.0732576 +14 77845228 1KG_14_77845228 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.504744:0.0:-0.224306 14 81366282 newrs147570461 C T . PASS . GT:GQ:BAF:LRR 0/0:0.494117:0.0:-0.025362 +14 81964337 1KG_14_81964337 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.305183:0.0:-0.240822 +14 88940031 1KG_14_88940031 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:-0.0926202 +14 88940112 1KG_14_88940112 A AT . PASS . GT:GQ:BAF:LRR 0/0:0.51473:0.0:-0.502162 +14 91444857 1KG_14_91444857 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.499884:0.0:-0.564836 14 92084075 newrs146758171 G A . PASS . GT:GQ:BAF:LRR 0/0:0.481477:0.0:0.0497337 +14 92466355 1KG_14_92466355 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.336045:0.0:-0.0214594 +14 92625397 1KG_14_92625397 T TA . PASS . GT:GQ:BAF:LRR 0/0:0.511834:0.0:0.00873225 14 93199039 newrs150780250 C T . PASS . GT:GQ:BAF:LRR 0/0:0.263703:0.0:0.028561 +14 93934131 1KG_14_93934131 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.498417:0.0:-0.496499 14 94752558 newrs149414832 G A . PASS . GT:GQ:BAF:LRR 0/0:0.517914:0.0:0.119721 +14 95562644 1KG_14_95562644 T TCAA . PASS . GT:GQ:BAF:LRR 0/0:0.497779:0.023280620575:-0.0920881 14 95658040 newrs150449481 G T . PASS . GT:GQ:BAF:LRR 0/0:0.411784:0.00872367620468:-0.0999293 14 96178607 newrs149840194 G A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.0720673 14 97342457 newrs149083861 C T . PASS . GT:GQ:BAF:LRR 0/0:0.512952:0.0:0.0249514 14 102822107 newrs150324463 A G . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.0:0.176048 14 105739057 newrs147262979 C T . PASS . GT:GQ:BAF:LRR 0/0:0.455851:0.0:0.278086 15 25971098 newrs148331114 C T . PASS . GT:GQ:BAF:LRR 0/0:0.396673:0.0:-0.083423 +15 26260492 1KG_15_26260492 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:0.0144477 15 28171292 newrs149648291 G A . PASS . GT:GQ:BAF:LRR 0/0:0.499187:0.0:-0.0508315 +15 31283029 1KG_15_31283029 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.00205433 +15 33091102 1KG_15_33091102 C CCTT . PASS . GT:GQ:BAF:LRR 0/0:0.518239:0.0:0.0329939 +15 33200716 1KG_15_33200716 G GTTC . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:-0.0413683 +15 34023840 1KG_15_34023840 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.386542:0.00296969:-0.169087 +15 34118459 1KG_15_34118459 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.485327:0.0:0.0248838 +15 34137079 1KG_15_34137079 T TAGA . PASS . GT:GQ:BAF:LRR 0/0:0.449994:0.00379556417465:0.161408 +15 40628005 1KG_15_40628005 C CCTT . PASS . GT:GQ:BAF:LRR 0/0:0.468641:0.0:0.237837 15 42445860 newrs150082965 T C . PASS . GT:GQ:BAF:LRR 0/0:0.518461:0.0:0.026474 15 42622872 newrs150469926 T G . PASS . GT:GQ:BAF:LRR 0/0:0.519141:0.0:-0.0477929 15 42684855 newrs149591108 T C . PASS . GT:GQ:BAF:LRR 0/0:0.458216:0.00720238:-1.07268 15 42703497 newrs149095128 C A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:-0.00834184 +15 42967877 1KG_15_42967877 T TGG . PASS . GT:GQ:BAF:LRR 0/0:0.467193:0.0:-0.214859 +15 43024569 1KG_15_43024569 T TGGGG . PASS . GT:GQ:BAF:LRR 0/0:0.472881:0.0316468:-0.559432 +15 43446900 1KG_15_43446900 T TTC . PASS . GT:GQ:BAF:LRR 0/0:0.514688:0.0:-0.00894402 +15 43533085 1KG_15_43533085 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.348161:0.0:-0.453429 +15 43699579 1KG_15_43699579 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.508848:0.0:0.0103217 +15 43816035 1KG_15_43816035 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.479895:0.0265371:-0.150846 15 44087615 newrs150100062 A C . PASS . GT:GQ:BAF:LRR 0/0:0.409735:0.0:0.0386938 +15 44881487 1KG_15_44881487 T TA . PASS . GT:GQ:BAF:LRR 0/0:0.518288:0.0:-0.0648148 15 44907685 newrs150434621 G A . PASS . GT:GQ:BAF:LRR 0/0:0.514317:0.00210070610046:0.0853994 +15 45050970 1KG_15_45050970 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.514753:0.0:0.0457818 +15 45444567 1KG_15_45444567 A ATC . PASS . GT:GQ:BAF:LRR 0/0:0.25593:0.0:0.105852 15 45454575 newrs148367370 G T . PASS . GT:GQ:BAF:LRR 0/0:0.494563:0.0147281885147:-0.514903 +15 49880279 1KG_15_49880279 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.494192:0.0:-0.576735 15 49924440 newrs146894806 G T . PASS . GT:GQ:BAF:LRR 0/0:0.468051:0.0:0.046572 15 50189488 newrs150777155 C T . PASS . GT:GQ:BAF:LRR 0/0:0.404719:0.0:-0.0245929 +15 52635367 1KG_15_52635367 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.501798:0.0:-0.391565 +15 59408899 1KG_15_59408899 T TTTC . PASS . GT:GQ:BAF:LRR 0/0:0.50585:0.00186038017273:-0.928104 +15 59417024 1KG_15_59417024 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.0041924 +15 59528839 1KG_15_59528839 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.398554:0.0:-0.529605 15 59911344 newrs149782376 C T . PASS . GT:GQ:BAF:LRR 0/0:0.413539:0.00940632820129:-0.272034 +15 59911594 1KG_15_59911594 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.445694:0.0:-0.0396788 15 62202414 newrs148074630 G A . PASS . GT:GQ:BAF:LRR 0/0:0.505129:0.0:0.101693 15 62210341 newrs149034021 G T . PASS . GT:GQ:BAF:LRR 0/0:0.51515:0.0:0.178682 +15 62325704 1KG_15_62325704 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.518081:0.000941574573517:0.20586 +15 63824875 1KG_15_63824875 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.268027:0.0937918:-0.779516 15 64701909 newrs147303485 C T . PASS . GT:GQ:BAF:LRR 0/0:0.508698:0.00782090425491:-0.597667 15 65447166 newrs148226354 C T . PASS . GT:GQ:BAF:LRR 0/0:0.331422:0.065142095089:-0.154789 +15 65490098 1KG_15_65490098 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.401146:0.0560216903687:-0.0244657 15 66606431 newrs150541699 C T . PASS . GT:GQ:BAF:LRR 0/0:0.509273:0.00178158283234:-0.119261 +15 66629455 1KG_15_66629455 C CTT . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.160656 +15 66832494 1KG_15_66832494 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.466035:0.0108358:-0.617936 +15 67571848 1KG_15_67571848 A AAGGTAGGTAT . PASS . GT:GQ:BAF:LRR 0/0:0.488997:0.0:-0.121833 +15 67664856 1KG_15_67664856 A AT . PASS . GT:GQ:BAF:LRR 0/0:0.487384:0.0252875685692:-0.312261 +15 69560685 1KG_15_69560685 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.053752 +15 69672338 1KG_15_69672338 G GCTGCC . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.0884788 +15 70959733 1KG_15_70959733 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.516059:0.0:0.0184608 +15 70975127 1KG_15_70975127 T TTC . PASS . GT:GQ:BAF:LRR 0/0:0.518048:0.0:-0.436906 15 71302182 newrs149193315 C T . PASS . GT:GQ:BAF:LRR 0/0:0.514607:0.0:0.334199 +15 71704117 1KG_15_71704117 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.374745:0.0222255587578:0.0838865 +15 72196372 1KG_15_72196372 T TA . PASS . GT:GQ:BAF:LRR 0/0:0.488494:0.0:-0.0110088 15 72637823 newrs147502219 T C . PASS . GT:GQ:BAF:LRR 0/0:0.50608:0.000414106:0.0405468 15 72699035 newrs146921317 C T . PASS . GT:GQ:BAF:LRR 0/0:0.49955:0.0:-0.064992 +15 73023724 1KG_15_73023724 T TGTGCTG . PASS . GT:GQ:BAF:LRR 0/0:0.490001:0.0:-0.0102512 15 75341568 newrs149414091 C T . PASS . GT:GQ:BAF:LRR 0/0:0.51178:0.0:0.147851 +15 75656827 1KG_15_75656827 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.547387 +15 75913246 1KG_15_75913246 T TTCCAGTAACC . PASS . GT:GQ:BAF:LRR 0/0:0.750527:0.0:0.00642419 +15 76254272 1KG_15_76254272 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.507115:0.0:-0.0523978 +15 78882503 1KG_15_78882503 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.0:0.138208 15 79220054 newrs148219875 C T . PASS . GT:GQ:BAF:LRR 0/0:0.416371:0.0:0.0682349 +15 81625560 1KG_15_81625560 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.41894:0.0:-0.294888 +15 83455619 1KG_15_83455619 G GCTT . PASS . GT:GQ:BAF:LRR 0/0:0.511439:0.0:-0.25492 15 85342440 newrs150829393 G A . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.00605225563049:0.109374 +15 87531320 1KG_15_87531320 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.384278:0.0:0.120131 +15 89444933 1KG_15_89444933 C CTGT . PASS . GT:GQ:BAF:LRR 0/0:0.856585:0.0:-0.0288526 15 89847147 newrs149464307 G A . PASS . GT:GQ:BAF:LRR 0/0:0.498335:0.0:-0.264452 +15 90150029 1KG_15_90150029 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.483202:0.0:-0.0638447 +15 90168090 1KG_15_90168090 T TCTC . PASS . GT:GQ:BAF:LRR 0/0:0.480417:0.0:-0.317644 +15 91524153 1KG_15_91524153 G GGCCACA . PASS . GT:GQ:BAF:LRR 0/0:0.508516:0.0:-0.287175 +15 91827317 1KG_15_91827317 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.383434:0.0:-0.214223 +15 99511804 1KG_15_99511804 A AC . PASS . GT:GQ:BAF:LRR 0/1:0.773975:0.47112:-0.282729 15 101113900 newrs149644940 A C . PASS . GT:GQ:BAF:LRR 0/0:0.518373:0.0:-0.116189 +15 101717654 1KG_15_101717654 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.497734:0.0:-0.0612846 15 101826419 newrs150109462 G A . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:-0.0377882 +15 102215928 1KG_15_102215928 T TTTC . PASS . GT:GQ:BAF:LRR 0/0:0.514785:0.0:-0.0942008 +16 682614 1KG_16_682614 C CGT . PASS . GT:GQ:BAF:LRR 0/0:0.490897:0.0:0.0794633 +16 733074 1KG_16_733074 T TA . PASS . GT:GQ:BAF:LRR 0/0:0.808284:0.00543463230133:0.128922 16 1827748 newrs147512809 C T . PASS . GT:GQ:BAF:LRR 0/0:0.480007:0.0:0.198985 +16 2235311 1KG_16_2235311 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.501277:0.0:0.262597 +16 2808514 1KG_16_2808514 C CAGA . PASS . GT:GQ:BAF:LRR 0/0:0.498006:0.0:0.0939984 +16 2813262 1KG_16_2813262 G GTCA . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.00649166107178:0.12858 16 3349792 newrs150368295 G A . PASS . GT:GQ:BAF:LRR 0/0:0.499756:0.0:0.134489 16 3807934 newrs148166625 T C . PASS . GT:GQ:BAF:LRR 0/0:0.467473:0.0375181:-0.178464 +16 4625464 1KG_16_4625464 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.458194:0.0:0.0897526 16 8905018 newrs150719105 T C . PASS . GT:GQ:BAF:LRR 0/0:0.517556:0.00773878:-0.821826 16 14024712 newrs150244523 T C . PASS . GT:GQ:BAF:LRR 0/0:0.831536:0.0186962:-0.0911935 16 14028147 newrs147458778 C T . PASS . GT:GQ:BAF:LRR 0/0:0.499078:0.0:-0.00703177 +16 15675155 1KG_16_15675155 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.45875:0.0:0.00888883 +16 19514867 1KG_16_19514867 C CTT . PASS . GT:GQ:BAF:LRR 0/0:0.409437:0.0037202835083:-0.0495282 16 19653798 newrs150266526 A G . PASS . GT:GQ:BAF:LRR 0/0:0.513806:0.0:-0.0783359 +16 20410570 1KG_16_20410570 A ACAG . PASS . GT:GQ:BAF:LRR 0/0:0.51428:0.0:-0.100078 +16 20681237 1KG_16_20681237 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.400639:0.0089208483696:-0.0609657 +16 20808206 1KG_16_20808206 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.511631:0.0:0.0705473 16 23767516 newrs147036175 T G . PASS . GT:GQ:BAF:LRR 0/0:0.511852:0.0152981:-0.341801 +16 25186337 1KG_16_25186337 A AAAG . PASS . GT:GQ:BAF:LRR 0/0:0.406094:0.00578018:-0.0162057 16 28890429 newrs150403167 C T . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.00239676237106:-0.323586 16 30017999 newrs150127737 C T . PASS . GT:GQ:BAF:LRR 0/0:0.465068:0.0:0.0318203 +16 30594708 1KG_16_30594708 CTTTTTGTTTT C . PASS . GT:GQ:BAF:LRR 0/0:0.431164:0.0:0.0113586 16 30596538 newrs147854775 C T . PASS . GT:GQ:BAF:LRR 0/0:0.371617:0.00957775115967:0.0818028 +16 30615597 1KG_16_30615597 G GCC . PASS . GT:GQ:BAF:LRR 0/0:0.5071:0.0:0.110368 16 30722073 newrs149689808 A G . PASS . GT:GQ:BAF:LRR 0/0:0.290874:0.0315611:0.151619 16 30770661 newrs150540962 A C . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.0637325 16 31196307 newrs148758737 G A . PASS . GT:GQ:BAF:LRR 0/0:0.211313:0.0998276472092:0.00334737 16 31418867 newrs147321998 C T . PASS . GT:GQ:BAF:LRR 0/0:0.475085:0.0:-0.25604 16 31425870 newrs149370240 C T . PASS . GT:GQ:BAF:LRR 0/0:0.506813:0.0:0.115725 +16 31427890 1KG_16_31427890 G GGT . PASS . GT:GQ:BAF:LRR 0/0:0.499806:0.0:-0.449556 +16 46744682 1KG_16_46744682 A ATGGGGAC . PASS . GT:GQ:BAF:LRR 0/0:0.412987:0.0:-0.0834948 +16 47117644 1KG_16_47117644 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.496835:0.0:0.126348 +16 47347676 1KG_16_47347676 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.489419:0.0:-0.0519229 16 47630364 newrs146634901 C T . PASS . GT:GQ:BAF:LRR 0/0:0.490858:0.0:-0.156925 +16 48174812 1KG_16_48174812 A AT . PASS . GT:GQ:BAF:LRR 0/0:0.42366:0.0:-0.000196934 16 48180230 newrs150215788 G A . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.213641 16 48249135 newrs150392452 C A . PASS . GT:GQ:BAF:LRR 0/0:0.506584:0.0:0.0827859 16 48385596 newrs150743514 C T . PASS . GT:GQ:BAF:LRR 0/0:0.509666:0.0:-0.25959 +16 50825518 1KG_16_50825518 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.513767:0.0303459763527:-1.01349 16 55608627 newrs149963829 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.053414 16 56534926 newrs147030232 G A . PASS . GT:GQ:BAF:LRR 0/0:0.383977:0.00260961055756:0.106897 +16 57503673 1KG_16_57503673 G GGT . PASS . GT:GQ:BAF:LRR 0/0:0.496463:0.0:-0.0472486 16 66976645 newrs147925730 T C . PASS . GT:GQ:BAF:LRR 0/0:0.490665:0.0:0.0619792 16 67226732 newrs148234724 C T . PASS . GT:GQ:BAF:LRR 0/0:0.310014:0.0:0.0547093 16 67646025 newrs147502048 G T . PASS . GT:GQ:BAF:LRR 0/0:0.469106:0.00348073244095:0.174057 +16 67699975 1KG_16_67699975 C CTCA . PASS . GT:GQ:BAF:LRR 0/0:0.495607:0.0:0.304828 16 67899132 newrs148843933 C T . PASS . GT:GQ:BAF:LRR 0/0:0.509894:0.0:0.204967 16 68105011 newrs148423881 C T . PASS . GT:GQ:BAF:LRR 0/0:0.891693:0.0:-0.00990669 +16 68732251 1KG_16_68732251 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.361645:0.0159124:0.0917653 16 68856057 newrs147925149 A G . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:0.180843 16 69366616 newrs147051782 C T . PASS . GT:GQ:BAF:LRR 0/0:0.518165:0.0:0.0258739 +16 70154432 1KG_16_70154432 C CAA . PASS . GT:GQ:BAF:LRR 0/0:0.401764:0.0:-0.0633051 16 70294970 newrs146946034 G A . PASS . GT:GQ:BAF:LRR 0/0:0.473455:0.0:0.106912 +16 71317544 1KG_16_71317544 T TTCTC . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:0.146713 16 71319742 newrs147189785 C A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.0076838 16 71483660 newrs147937440 G A . PASS . GT:GQ:BAF:LRR 0/0:0.432874:0.0:0.0446202 16 72015958 newrs150292834 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500203:0.0:0.0924446 +16 75512539 1KG_16_75512539 C CTAA . PASS . GT:GQ:BAF:LRR 0/0:0.478128:0.0329943299294:-0.498449 16 78062087 newrs149263151 G A . PASS . GT:GQ:BAF:LRR 0/0:0.499127:0.0:-0.194631 +16 81303791 1KG_16_81303791 A ACCAGGCAG . PASS . GT:GQ:BAF:LRR 0/0:0.449554:0.0:-0.650519 +16 84005773 1KG_16_84005773 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.0201837 16 84012119 newrs147214689 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519052:0.0:0.156354 +16 84514302 1KG_16_84514302 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.468913:0.0:-0.0112286 +16 87795599 1KG_16_87795599 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.39483:0.0:0.092453 16 88926138 newrs147583352 C T . PASS . GT:GQ:BAF:LRR ./.:0.0774364:0.0992125272751:0.0320451 16 89805351 newrs149851163 C T . PASS . GT:GQ:BAF:LRR 0/0:0.516748:0.0:0.0987733 +16 90038228 1KG_16_90038228 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.908585:0.00210738182068:0.103503 17 263221 newrs147094351 G A . PASS . GT:GQ:BAF:LRR 0/0:0.40356:0.000976324081421:0.192712 17 1562030 newrs147690140 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.00343453884125:-0.177816 17 2227800 newrs147919745 A C . PASS . GT:GQ:BAF:LRR 0/0:0.336045:0.0:0.185958 +17 4060189 1KG_17_4060189 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.351044:0.0:0.0472225 +17 4074072 1KG_17_4074072 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.450884:0.030641:-0.708735 +17 4836675 1KG_17_4836675 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:-0.00275607 +17 6483140 1KG_17_6483140 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.446922:0.0:-0.153426 +17 9757838 1KG_17_9757838 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:-0.0786165 17 10304221 newrs150717297 C A . PASS . GT:GQ:BAF:LRR 0/0:0.507941:0.0:-0.452055 17 10348553 newrs149888634 C T . PASS . GT:GQ:BAF:LRR 0/0:0.497929:0.00817453861237:-0.140879 17 10408830 newrs150031915 T C . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:-0.1808 17 10595189 newrs149824738 C T . PASS . GT:GQ:BAF:LRR 0/0:0.514046:0.0:0.177347 +17 15215597 1KG_17_15215597 C CTTA . PASS . GT:GQ:BAF:LRR 0/0:0.479432:0.0134572386742:0.0450782 +17 15458599 1KG_17_15458599 A AT . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.0:-0.0808854 17 17106264 newrs150565127 G A . PASS . GT:GQ:BAF:LRR 0/0:0.376958:0.0:0.202396 +17 18156752 1KG_17_18156752 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.49787:0.0:-0.445918 17 19839690 newrs148949492 A C . PASS . GT:GQ:BAF:LRR 0/0:0.4534:0.0:-0.175886 +17 26856198 1KG_17_26856198 C CGATGGGCA . PASS . GT:GQ:BAF:LRR 0/0:0.481231:0.0:0.0913962 17 26911669 newrs149791493 C T . PASS . GT:GQ:BAF:LRR 0/0:0.231727:0.0664598345757:-0.0365607 17 26951283 newrs148098359 G A . PASS . GT:GQ:BAF:LRR 0/0:0.487028:0.0:-0.0464276 17 26966331 newrs146835965 A C . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.0596718 17 27371895 newrs148923684 C T . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.117691 +17 28445103 1KG_17_28445103 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.480967:0.0:-0.122732 17 29187450 newrs149775337 G T . PASS . GT:GQ:BAF:LRR 0/0:0.222323:0.0850291252136:-0.936643 +17 29221149 1KG_17_29221149 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.514735:0.0:0.185768 +17 33738533 1KG_17_33738533 A AT . PASS . GT:GQ:BAF:LRR 0/0:0.50363:0.0:0.15746 17 35310470 newrs146758318 C T . PASS . GT:GQ:BAF:LRR 0/0:0.346175:0.0127606391907:0.0373722 17 35578764 newrs147589959 C T . PASS . GT:GQ:BAF:LRR 0/0:0.504503:0.0:0.103574 17 35993449 newrs149632848 C A . PASS . GT:GQ:BAF:LRR ./.:0.133786:0.105671346188:-0.578131 +17 36551637 1KG_17_36551637 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.389878:0.0:0.0856874 +17 38857459 1KG_17_38857459 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.492916:0.0:-0.369364 +17 39657611 1KG_17_39657611 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.738994:0.0:-0.142286 +17 39739365 1KG_17_39739365 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.0:-0.0729028 +17 40011269 1KG_17_40011269 A ATC . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:0.0256087 +17 40344302 1KG_17_40344302 G GCAC . PASS . GT:GQ:BAF:LRR 0/0:0.467283:0.0:0.0423988 17 40725496 newrs150572842 C T . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.00196558237076:0.0363982 +17 40911775 1KG_17_40911775 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.511852:0.0:-0.113872 17 44248642 newrs149830411 G A . PASS . GT:GQ:BAF:LRR 0/0:0.516895:0.0:-0.337851 +17 45479497 1KG_17_45479497 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.896927:0.0:0.134843 17 45909571 newrs146752078 T C . PASS . GT:GQ:BAF:LRR 0/0:0.412812:0.0:-0.00522992 17 46799678 newrs150679020 A G . PASS . GT:GQ:BAF:LRR 0/0:0.412812:0.0:0.210182 17 47700131 newrs150193528 C T . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.0:-0.00589858 +17 48692778 1KG_17_48692778 C CACTTGTGCA . PASS . GT:GQ:BAF:LRR 0/0:0.480417:0.031800031662:-0.215044 17 52991116 newrs148143284 C A . PASS . GT:GQ:BAF:LRR 0/0:0.372283:0.000627636909485:0.0788764 +17 53016308 1KG_17_53016308 G GTTTAAGTTGTT . PASS . GT:GQ:BAF:LRR 0/0:0.838018:0.0:0.105219 +17 56350827 1KG_17_56350827 G GGGGTTGGGTTCCAT . PASS . GT:GQ:BAF:LRR 0/0:0.464693:0.0:-0.00580283 17 58303400 newrs147383770 C T . PASS . GT:GQ:BAF:LRR 0/0:0.493171:0.0:-0.166292 +17 60642432 1KG_17_60642432 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.376958:0.0068531036377:0.059663 +17 61391850 1KG_17_61391850 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.417656:0.0184135437012:-0.84521 +17 62142597 1KG_17_62142597 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.0:0.0974742 +17 63052550 1KG_17_63052550 CAGCAGCAGGATCTTCA C . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:-0.128985 17 63898371 newrs147238839 G A . PASS . GT:GQ:BAF:LRR 0/0:0.43318:0.000779747962952:-0.106356 +17 64219860 1KG_17_64219860 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.485874:0.0:0.0150813 +17 65960358 1KG_17_65960358 T TTGGTACCATGGGC . PASS . GT:GQ:BAF:LRR 0/0:0.447064:0.00766003131866:0.0635465 17 66251877 newrs149406006 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.104402 17 67014554 newrs146820712 C T . PASS . GT:GQ:BAF:LRR 0/0:0.510942:0.0:-0.317105 17 67079352 newrs149614799 C T . PASS . GT:GQ:BAF:LRR 0/0:0.515898:0.0:-0.0328294 +17 67109843 1KG_17_67109843 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.47628:0.0:0.0821045 +17 72211845 1KG_17_72211845 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.4908:0.0:-0.0961057 17 73035125 newrs148887046 G A . PASS . GT:GQ:BAF:LRR 0/0:0.374745:0.0:0.161957 17 73049198 newrs150354933 C T . PASS . GT:GQ:BAF:LRR 0/0:0.406248:0.0:0.162869 17 74574836 newrs146729471 A G . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.167866 +17 78078836 1KG_17_78078836 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.486857:0.0:0.0258881 17 78341873 newrs149974667 C T . PASS . GT:GQ:BAF:LRR 0/0:0.511852:0.0:0.162846 +17 79994114 1KG_17_79994114 TG T . PASS . GT:GQ:BAF:LRR 0/0:0.49841:0.0:-0.00269577 17 80972329 newrs146876805 C T . PASS . GT:GQ:BAF:LRR 0/0:0.882836:0.00267112255096:-0.0563226 +18 580600 1KG_18_580600 C CAGGA . PASS . GT:GQ:BAF:LRR 0/0:0.390566:0.00411981344223:0.117925 +18 2778209 1KG_18_2778209 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.487295:0.0:-0.178348 +18 6887226 1KG_18_6887226 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.499439:0.0:-0.179175 +18 8545714 1KG_18_8545714 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.232102 +18 10532770 1KG_18_10532770 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.4901:0.00238573551178:0.249261 +18 12546737 1KG_18_12546737 C CCTT . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.0:-0.00290642 18 13114210 newrs149673520 C T . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:0.0731197 +18 19426916 1KG_18_19426916 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.399195:0.0:-0.0485253 +18 21113458 1KG_18_21113458 T TGTAA . PASS . GT:GQ:BAF:LRR 0/0:0.511852:0.0:0.129571 +18 28989728 1KG_18_28989728 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.311626:0.0221352:-0.179592 +18 28991360 1KG_18_28991360 C CTA . PASS . GT:GQ:BAF:LRR 0/0:0.405018:0.00500047206879:-0.145848 +18 29125917 1KG_18_29125917 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.361595:0.0118274:-0.183223 +18 29782937 1KG_18_29782937 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.517819:0.0:-0.1606 +18 33751035 1KG_18_33751035 T TG . PASS . GT:GQ:BAF:LRR ./.:0.0717921:0.09808:-0.383365 18 33754535 newrs146555723 G A . PASS . GT:GQ:BAF:LRR 0/0:0.505147:0.0:-0.36685 18 43262283 newrs147596856 G A . PASS . GT:GQ:BAF:LRR 0/0:0.322317:0.0582450032234:0.071208 +18 43529517 1KG_18_43529517 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.24899 +18 44113212 1KG_18_44113212 G GT . PASS . GT:GQ:BAF:LRR ./.:0.0:0.175199866295:-0.197686 +18 44416367 1KG_18_44416367 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.501152:0.0:-0.0388367 +18 44626644 1KG_18_44626644 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.411604:0.0:-0.365015 +18 47010064 1KG_18_47010064 A AT . PASS . GT:GQ:BAF:LRR 0/0:0.508981:0.0:-0.244343 18 47311566 newrs147811299 C T . PASS . GT:GQ:BAF:LRR 0/0:0.517677:0.0:0.160541 18 48333089 newrs148800283 A C . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:0.075275 +18 51889291 1KG_18_51889291 T TGTAA . PASS . GT:GQ:BAF:LRR 0/0:0.518891:0.0:0.160987 18 52586573 newrs149563439 G A . PASS . GT:GQ:BAF:LRR 0/0:0.458079:0.0:0.043438 +18 55319396 1KG_18_55319396 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.382762:0.0:0.0602788 +18 55833055 1KG_18_55833055 T TGG . PASS . GT:GQ:BAF:LRR 0/0:0.511799:0.0:-0.0528158 +18 56247773 1KG_18_56247773 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.351044:0.0:0.0393908 +18 56897667 1KG_18_56897667 T TGAAG . PASS . GT:GQ:BAF:LRR 0/0:0.430131:0.000504402:-0.0817439 +18 59941236 1KG_18_59941236 T TG . PASS . GT:GQ:BAF:LRR 0/0:0.483202:0.0:0.0360835 18 61569116 newrs150189388 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.0273585 +18 61582826 1KG_18_61582826 A ATCT . PASS . GT:GQ:BAF:LRR 0/0:0.507142:0.0:-0.711148 +18 61597290 1KG_18_61597290 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.499724:0.0:-0.0325777 +18 72247400 1KG_18_72247400 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.514438:0.00479447841644:-0.102013 +18 72344969 1KG_18_72344969 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.510929:0.0:-0.0990774 +18 72914191 1KG_18_72914191 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.487321:0.00756636:-0.907233 +18 74637379 1KG_18_74637379 A ACCT . PASS . GT:GQ:BAF:LRR 0/0:0.365928:0.0:-0.0515706 +18 76856649 1KG_18_76856649 G GGT . PASS . GT:GQ:BAF:LRR 0/0:0.480596:0.00543616:-0.842979 18 77104307 newrs147932692 C T . PASS . GT:GQ:BAF:LRR 0/0:0.459337:0.0157560110092:0.0249785 +18 77894966 1KG_18_77894966 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.349231:0.0:-0.192118 +19 815834 1KG_19_815834 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.402859:0.0:0.149432 19 2853204 newrs150017916 C T . PASS . GT:GQ:BAF:LRR 0/0:0.497155:0.0:-0.0936644 19 2877866 newrs148855297 C T . PASS . GT:GQ:BAF:LRR 0/0:0.374566:0.00668179988861:-0.344505 19 2934107 newrs146879198 G A . PASS . GT:GQ:BAF:LRR 0/0:0.50868:0.00336682796478:0.093836 +19 6177274 1KG_19_6177274 T TTAAAC . PASS . GT:GQ:BAF:LRR 0/0:0.463466:0.0:0.138896 19 6366374 newrs147589840 G A . PASS . GT:GQ:BAF:LRR 0/0:0.402133:0.0:0.247399 19 8152712 newrs150404330 G A . PASS . GT:GQ:BAF:LRR 0/0:0.474595:0.0:-0.0923076 19 8979212 newrs149481309 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500971:0.0:0.00342115 19 9237120 newrs149823005 G T . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:0.106778 +19 9452492 1KG_19_9452492 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.311597:0.0:0.102071 19 9453655 newrs147456906 C T . PASS . GT:GQ:BAF:LRR 0/0:0.890395:0.0:0.0189498 19 9526374 newrs146586902 G A . PASS . GT:GQ:BAF:LRR 0/0:0.487353:0.0267685651779:0.0685457 19 10103502 newrs149888433 C T . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.147785 19 11227666 newrs148181903 G A . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:-0.0392318 +19 11728704 1KG_19_11728704 A AGC . PASS . GT:GQ:BAF:LRR 0/0:0.894589:0.0:0.0271545 19 12015703 newrs148289998 G A . PASS . GT:GQ:BAF:LRR 0/0:0.163365:0.0:0.0659004 19 12298163 newrs149038305 C T . PASS . GT:GQ:BAF:LRR 0/0:0.484988:0.0:0.0977261 19 12298190 newrs148282298 G T . PASS . GT:GQ:BAF:LRR 0/0:0.486917:0.0:0.15965 @@ -913,8 +1810,10 @@ 19 12430286 newrs150045277 G A . PASS . GT:GQ:BAF:LRR 0/0:0.462629:0.0:0.0432913 19 12460637 newrs147649018 G A . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:0.127913 19 14748918 newrs149254238 G A . PASS . GT:GQ:BAF:LRR 0/0:0.429903:0.0:0.036748 +19 16040331 1KG_19_16040331 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.463058:0.0:-0.0724683 19 16612192 newrs148952679 C T . PASS . GT:GQ:BAF:LRR 0/0:0.465715:0.000305891036987:-0.0132468 19 17628609 newrs148238828 C T . PASS . GT:GQ:BAF:LRR 0/0:0.498638:0.0:0.242315 +19 18121046 1KG_19_18121046 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.442729:0.0:0.130179 19 18423437 newrs147169736 G A . PASS . GT:GQ:BAF:LRR 0/0:0.43126:0.0:0.0932386 19 19304942 newrs150525759 G A . PASS . GT:GQ:BAF:LRR 0/0:0.517259:0.0:-0.0574026 19 19822451 newrs150668126 G A . PASS . GT:GQ:BAF:LRR 0/0:0.41267:0.0:0.0153763 @@ -926,6 +1825,7 @@ 19 34890477 newrs148811525 G A . PASS . GT:GQ:BAF:LRR 0/0:0.45385:0.0:0.0267558 19 35251195 newrs150001961 G A . PASS . GT:GQ:BAF:LRR 0/0:0.498791:0.00469571352005:-0.38209 19 35979712 newrs149292016 G A . PASS . GT:GQ:BAF:LRR 0/0:0.405942:0.0:0.0529032 +19 36029498 1KG_19_36029498 A ACT . PASS . GT:GQ:BAF:LRR 0/0:0.508433:0.0:-0.19523 19 36636905 newrs148900101 C T . PASS . GT:GQ:BAF:LRR 0/0:0.514213:0.0:0.0542241 19 37005949 newrs149550734 G T . PASS . GT:GQ:BAF:LRR 0/0:0.499997:0.0:0.165992 19 37309679 newrs147371360 G A . PASS . GT:GQ:BAF:LRR 0/0:0.467707:0.0:-0.0473625 @@ -936,31 +1836,60 @@ 19 38160389 newrs147935289 C A . PASS . GT:GQ:BAF:LRR ./.:0.00387779:0.192010521889:-0.153111 19 38230107 newrs149484261 G T . PASS . GT:GQ:BAF:LRR 0/0:0.494433:0.0:0.0136336 19 38945887 newrs147723844 A G . PASS . GT:GQ:BAF:LRR 0/0:0.711998:0.0:0.145316 +19 38948158 1KG_19_38948158 C CTG . PASS . GT:GQ:BAF:LRR 0/0:0.290874:0.0:0.192841 19 39034005 newrs148399313 G A . PASS . GT:GQ:BAF:LRR 0/0:0.439902:0.0:0.0461478 19 39076780 newrs146876145 C T . PASS . GT:GQ:BAF:LRR 0/0:0.482913:0.00675463676453:-0.262015 19 40197274 newrs150238702 C A . PASS . GT:GQ:BAF:LRR 0/0:0.32364:0.0:-0.00544655 19 40580545 newrs149702621 G A . PASS . GT:GQ:BAF:LRR 0/0:0.360361:0.0:-0.150464 19 40580629 newrs147947129 G A . PASS . GT:GQ:BAF:LRR 0/0:0.3047:0.0:-0.0823699 +19 41216025 1KG_19_41216025 C CAAGCCCA . PASS . GT:GQ:BAF:LRR 0/0:0.376958:0.0:0.0906996 +19 41627432 1KG_19_41627432 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.249804:0.0:0.250673 19 41920067 newrs149899007 G A . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:0.0918607 19 42190820 newrs150439369 C A . PASS . GT:GQ:BAF:LRR 0/0:0.381426:0.0217183828354:-0.200623 +19 42753148 1KG_19_42753148 G GGAA . PASS . GT:GQ:BAF:LRR 0/0:0.453283:0.0:0.352262 +19 42801356 1KG_19_42801356 C CAT . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.219831 19 43699204 newrs147584129 C A . PASS . GT:GQ:BAF:LRR 0/0:0.461736:0.0:-0.0188369 19 43762499 newrs150777161 C T . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:-0.0222313 19 43771960 newrs146901255 G A . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:-0.253375 19 44280789 newrs147965350 C T . PASS . GT:GQ:BAF:LRR 0/0:0.474791:0.0382894277573:0.0832743 19 44500621 newrs147279924 T G . PASS . GT:GQ:BAF:LRR 0/0:0.517605:0.0:-0.30084 +19 44832396 1KG_19_44832396 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.355193:0.0407398939133:-0.0391361 +19 44982104 1KG_19_44982104 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.368189:0.0103741884232:-0.589216 +19 45862120 1KG_19_45862120 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.448513:0.0:-0.180327 +19 46181014 1KG_19_46181014 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.346175:0.0:0.129858 +19 48593621 1KG_19_48593621 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.0345953 +19 48836477 1KG_19_48836477 C CAGG . PASS . GT:GQ:BAF:LRR 0/0:0.427353:0.0:0.00514873 19 49341353 newrs150707206 G A . PASS . GT:GQ:BAF:LRR 0/0:0.499477:0.0:-0.0328186 +19 50046417 1KG_19_50046417 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.399569:0.0:-0.391951 +19 50963307 1KG_19_50963307 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.467283:0.0:-0.0111731 +19 51135999 1KG_19_51135999 A AAG . PASS . GT:GQ:BAF:LRR 0/0:0.361723:0.00960462:0.222817 +19 52089923 1KG_19_52089923 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.515577:0.0:-0.222294 19 58099976 newrs148725359 C T . PASS . GT:GQ:BAF:LRR 0/0:0.196519:0.0:0.0264718 +19 58115759 1KG_19_58115759 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.37932:0.0610456466675:-0.116933 19 58146047 newrs147342045 G A . PASS . GT:GQ:BAF:LRR 0/0:0.506865:0.0:-0.0435322 +19 58301766 newrs149669568 TG T . PASS . GT:GQ:BAF:LRR 0/0:0.168655:0.00497269630432:-0.00942363 19 58578441 newrs148932599 G T . PASS . GT:GQ:BAF:LRR 0/0:0.410472:0.0:-0.202507 +20 1456961 1KG_20_1456961 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.422901:0.0:0.0201305 20 1961587 newrs149872114 G T . PASS . GT:GQ:BAF:LRR 0/0:0.519086:0.0:-0.151775 +20 2290830 1KG_20_2290830 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.386838:0.0:0.159118 +20 2818989 1KG_20_2818989 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:-0.0990324 20 3210383 newrs150571742 T C . PASS . GT:GQ:BAF:LRR 0/0:0.463099:0.0:0.034672 +20 5903282 1KG_20_5903282 T TGAG . PASS . GT:GQ:BAF:LRR 0/0:0.327091:0.0:-0.0998198 +20 6091082 1KG_20_6091082 C CATG . PASS . GT:GQ:BAF:LRR 0/0:0.483202:0.0:-0.276408 20 8626828 newrs148738915 C T . PASS . GT:GQ:BAF:LRR 0/0:0.503645:0.0:-0.656115 20 10386055 newrs149051148 C T . PASS . GT:GQ:BAF:LRR 0/0:0.823464:0.0:-0.066093 20 10393273 newrs147704542 A G . PASS . GT:GQ:BAF:LRR 0/0:0.51201:0.0:-0.13239 20 10582468 newrs148856218 G A . PASS . GT:GQ:BAF:LRR 0/0:0.518749:0.0:-0.139811 +20 13740447 1KG_20_13740447 C CCTT . PASS . GT:GQ:BAF:LRR 0/0:0.493432:0.0:0.226828 20 16359919 newrs148283912 G A . PASS . GT:GQ:BAF:LRR 0/0:0.436915:0.0:0.011523 +20 16407800 1KG_20_16407800 G GGGACCCA . PASS . GT:GQ:BAF:LRR 0/0:0.799765:0.0:-0.165518 20 16488602 newrs147318741 C T . PASS . GT:GQ:BAF:LRR 0/0:0.44896:0.0:-0.0658218 +20 16729654 1KG_20_16729654 A AAGATG . PASS . GT:GQ:BAF:LRR 0/1:0.848497:0.43275:-0.301323 +20 17389951 1KG_20_17389951 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.416528:0.0:0.173674 +20 20007457 1KG_20_20007457 A AG . PASS . GT:GQ:BAF:LRR 0/0:0.483127:0.0:-0.0420362 20 20180478 newrs147638085 C T . PASS . GT:GQ:BAF:LRR 0/0:0.43418:0.0:-0.314772 +20 20620509 1KG_20_20620509 G GTAGGA . PASS . GT:GQ:BAF:LRR 0/0:0.482914:0.0:-0.202484 +20 25434092 1KG_20_25434092 C CAG . PASS . GT:GQ:BAF:LRR 0/0:0.487682:0.00255751609802:0.0343977 20 25484742 newrs150265900 T C . PASS . GT:GQ:BAF:LRR 0/0:0.361595:0.0:-0.229587 20 29965124 newrs146735308 G T . PASS . GT:GQ:BAF:LRR 0/0:0.456015:0.0:0.0810949 20 30616808 newrs149235259 C T . PASS . GT:GQ:BAF:LRR 0/0:0.449635:0.0:0.0314867 @@ -968,46 +1897,101 @@ 20 31388016 newrs146981624 T C . PASS . GT:GQ:BAF:LRR 0/0:0.348161:0.000381047:0.0353587 20 31572946 newrs147686372 G A . PASS . GT:GQ:BAF:LRR 0/0:0.516114:0.0:0.0245875 20 31954730 newrs148992921 G A . PASS . GT:GQ:BAF:LRR 0/0:0.412879:0.0:-0.0692842 +20 34241569 1KG_20_34241569 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:0.048361 +20 34242272 1KG_20_34242272 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.499764:0.0:-0.76287 20 35526320 newrs149846637 G A . PASS . GT:GQ:BAF:LRR 0/0:0.506012:0.00400620698929:0.0680538 20 36953197 newrs150749170 C T . PASS . GT:GQ:BAF:LRR 0/0:0.494166:0.0:-0.396903 +20 37182604 1KG_20_37182604 A AGAG . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:-0.21342 +20 42826009 1KG_20_42826009 C CTGAT . PASS . GT:GQ:BAF:LRR 0/0:0.41782:0.000722944736481:0.00548835 +20 43249673 1KG_20_43249673 C CCTCTT . PASS . GT:GQ:BAF:LRR 0/0:0.485732:0.0:-0.130105 20 43629072 newrs148138374 C T . PASS . GT:GQ:BAF:LRR 0/0:0.529569:0.0:-0.112961 20 43837202 newrs147667060 C T . PASS . GT:GQ:BAF:LRR 0/0:0.497983:0.0:-0.127842 20 44141410 newrs148191315 G A . PASS . GT:GQ:BAF:LRR 0/0:0.872238:0.0:0.0923713 20 49576632 newrs149569136 C A . PASS . GT:GQ:BAF:LRR 0/0:0.484587:0.0:-0.036793 20 53266980 newrs148201917 C T . PASS . GT:GQ:BAF:LRR 0/0:0.410906:0.00440800189972:0.0526855 +20 57767938 1KG_20_57767938 G GTGTAC . PASS . GT:GQ:BAF:LRR 0/0:0.371617:0.0:0.0650136 +20 58567455 1KG_20_58567455 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.508554:0.0:-0.144078 +20 58587783 1KG_20_58587783 TA T . PASS . GT:GQ:BAF:LRR 0/0:0.468853:0.0:0.0472306 +20 62127324 1KG_20_62127324 C CCGCGCT . PASS . GT:GQ:BAF:LRR 0/0:0.381782:0.0:0.228685 20 62851132 newrs150660744 G T . PASS . GT:GQ:BAF:LRR 0/0:0.376958:0.0:0.0333837 +21 30378845 1KG_21_30378845 T TAACACTG . PASS . GT:GQ:BAF:LRR 0/0:0.505955:0.0:-0.8201 21 31538770 newrs148594408 G A . PASS . GT:GQ:BAF:LRR 0/0:0.518862:0.0:-0.0526677 +21 31655154 1KG_21_31655154 T TA . PASS . GT:GQ:BAF:LRR 0/0:0.499908:0.0:0.0899807 +21 31971075 1KG_21_31971075 T TA . PASS . GT:GQ:BAF:LRR 0/0:0.728902:0.0139644145966:-0.0649513 21 32119310 newrs147814118 G A . PASS . GT:GQ:BAF:LRR 0/0:0.512012:0.0:0.0954213 +21 34029016 1KG_21_34029016 C CA . PASS . GT:GQ:BAF:LRR 0/0:0.502616:0.0:-0.0622662 21 34950699 newrs147521584 C T . PASS . GT:GQ:BAF:LRR 0/0:0.508082:0.0:-0.104971 +21 35276312 1KG_21_35276312 G GCTT . PASS . GT:GQ:BAF:LRR 0/0:0.513433:0.0133957266808:-0.124457 21 35742857 newrs148968498 G A . PASS . GT:GQ:BAF:LRR 0/0:0.482174:0.0:-0.297359 21 37408510 newrs148061279 G A . PASS . GT:GQ:BAF:LRR 0/0:0.461888:0.00132811069489:0.0176279 +21 37445160 1KG_21_37445160 A AAG . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.02063 21 38128952 newrs149399432 C T . PASS . GT:GQ:BAF:LRR 0/0:0.429459:0.0:0.092287 +21 39774538 1KG_21_39774538 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.496142:0.0:-0.411884 +21 40646312 1KG_21_40646312 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.409447:0.00404620170593:0.110697 +21 40778153 1KG_21_40778153 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.330024:0.00793131:-0.943974 21 42821222 newrs148192027 G A . PASS . GT:GQ:BAF:LRR 0/0:0.503574:0.0:-0.157748 +21 43412988 1KG_21_43412988 C CGAT . PASS . GT:GQ:BAF:LRR 0/0:0.869842:0.00840449333191:0.0906655 21 43862591 newrs148203332 C T . PASS . GT:GQ:BAF:LRR 0/0:0.454809:0.0:0.0516431 +21 44192622 1KG_21_44192622 A AC . PASS . GT:GQ:BAF:LRR 0/0:0.495709:0.0:-0.521884 21 44323380 newrs148055450 C A . PASS . GT:GQ:BAF:LRR 0/0:0.5153:0.00846242904663:0.167604 21 46314884 newrs149804560 A G . PASS . GT:GQ:BAF:LRR 0/0:0.500064:0.0:0.142767 +22 19766749 1KG_22_19766749 A AT . PASS . GT:GQ:BAF:LRR 0/0:0.498632:0.0:-0.212669 22 20907430 newrs149792139 A C . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:0.0194699 +22 24530438 1KG_22_24530438 G GA . PASS . GT:GQ:BAF:LRR 0/0:0.478458:0.0054258108139:0.0180235 +22 24909316 1KG_22_24909316 G GT . PASS . GT:GQ:BAF:LRR 0/0:0.416056:0.0:0.102206 22 26114280 newrs148927409 C T . PASS . GT:GQ:BAF:LRR 0/0:0.417444:0.0:0.108142 +22 26298671 1KG_22_26298671 T TGG . PASS . GT:GQ:BAF:LRR 0/0:0.467283:0.0:-0.120359 22 29130534 newrs149991239 G T . PASS . GT:GQ:BAF:LRR 0/0:0.506522:0.0:0.0857932 22 29456783 newrs146955915 G A . PASS . GT:GQ:BAF:LRR 0/0:0.519144:0.0:-0.377919 +22 29886187 1KG_22_29886187 C CAG . PASS . GT:GQ:BAF:LRR 0/0:0.186524:0.0:0.071159 +22 30857665 1KG_22_30857665 T TCC . PASS . GT:GQ:BAF:LRR 0/0:0.446922:0.0:-0.357796 22 32792056 newrs146836672 T C . PASS . GT:GQ:BAF:LRR 0/0:0.472745:0.0:0.0513183 22 36653372 newrs149411999 C T . PASS . GT:GQ:BAF:LRR 0/0:0.423935:0.0:-0.022094 +22 36681998 1KG_22_36681998 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.483202:0.0:0.0763452 +22 38494134 1KG_22_38494134 T TC . PASS . GT:GQ:BAF:LRR 0/0:0.361679:0.0:0.271236 22 39148627 newrs148700122 G A . PASS . GT:GQ:BAF:LRR 0/0:0.494921:0.0:0.145634 +22 40661826 1KG_22_40661826 C CAA . PASS . GT:GQ:BAF:LRR 0/0:0.494062:0.00161391496658:-0.082693 +22 41188600 1KG_22_41188600 C CT . PASS . GT:GQ:BAF:LRR 0/0:0.516664:0.0:0.181358 22 41188676 newrs147898473 C T . PASS . GT:GQ:BAF:LRR 0/0:0.367053:0.00573420524597:0.0638442 22 41305124 newrs149609214 A G . PASS . GT:GQ:BAF:LRR 0/0:0.401561:0.0:-0.0169839 22 41605795 newrs146730690 G A . PASS . GT:GQ:BAF:LRR 0/0:0.410227:0.0:0.0657953 22 41863452 newrs148099525 G A . PASS . GT:GQ:BAF:LRR 0/0:0.529569:0.0:-0.184435 22 43464415 newrs146662174 C T . PASS . GT:GQ:BAF:LRR 0/0:0.500205:0.0:0.195691 +22 43926808 1KG_22_43926808 C CAGAGT . PASS . GT:GQ:BAF:LRR 0/0:0.516234:0.0:0.130747 +22 45749876 1KG_22_45749876 G GC . PASS . GT:GQ:BAF:LRR 0/0:0.473406:0.0:-0.229495 X 3241377 newrs150681202 C T . PASS . GT:GQ:BAF:LRR 0:0.401561:0.0:0.0395558 +X 13734617 1KG_X_13734617 T TTTAG . PASS . GT:GQ:BAF:LRR 0:0.392839:0.0:0.0682034 +X 21450738 1KG_X_21450738 C CT . PASS . GT:GQ:BAF:LRR 0:0.497315:0.0:0.0817721 +X 24552048 1KG_X_24552048 T TC . PASS . GT:GQ:BAF:LRR 0:0.512127:0.00540852:-0.401194 +X 31854853 1KG_X_31854853 T TG . PASS . GT:GQ:BAF:LRR 0:0.511852:0.00353288:0.0390732 X 44950109 newrs148188315 A G . PASS . GT:GQ:BAF:LRR 0:0.513279:0.0:-0.202387 +X 50089739 1KG_X_50089739 T TC . PASS . GT:GQ:BAF:LRR 0:0.390414:0.0017099:-0.0203266 X 62917005 newrs150129110 G A . PASS . GT:GQ:BAF:LRR 0:0.513773:0.0:0.0654194 +X 63410214 1KG_X_63410214 T TG . PASS . GT:GQ:BAF:LRR 0:0.462962:0.0:-0.287109 X 63445212 newrs148346736 G A . PASS . GT:GQ:BAF:LRR 0:0.419945:0.0:-0.0193036 +X 63445311 1KG_X_63445311 CAGGAACA C . PASS . GT:GQ:BAF:LRR 0:0.386838:0.0:0.00502534 +X 69504438 1KG_X_69504438 C CG . PASS . GT:GQ:BAF:LRR 0:0.265879:0.0389524:-0.751128 +X 71359531 1KG_X_71359531 CTCCAGTGGCTACT C . PASS . GT:GQ:BAF:LRR 0:0.379837:0.0:-0.0441196 X 73524476 newrs149628222 C A . PASS . GT:GQ:BAF:LRR 0:0.508385:0.0:-0.213667 X 101091706 newrs146841797 C A . PASS . GT:GQ:BAF:LRR 0:0.388738:0.00501638650894:0.0018265 +X 102841669 1KG_X_102841669 A AC . PASS . GT:GQ:BAF:LRR 0:0.500205:0.0:0.101279 +X 105937283 1KG_X_105937283 C CT . PASS . GT:GQ:BAF:LRR 0:0.497823:0.0:-0.0256053 +X 106228437 1KG_X_106228437 AGGCTG A . PASS . GT:GQ:BAF:LRR 0:0.505512:0.0:-0.377681 X 106331799 newrs149164060 C T . PASS . GT:GQ:BAF:LRR 0:0.464871:0.0:0.00401862 +X 110497554 1KG_X_110497554 C CTT . PASS . GT:GQ:BAF:LRR 0:0.511323:0.0:-0.000705043 X 111698143 newrs148205998 C T . PASS . GT:GQ:BAF:LRR 0:0.516643:0.0:0.0937407 +X 122766713 1KG_X_122766713 T TG . PASS . GT:GQ:BAF:LRR 0:0.446922:0.0:0.06041 +X 129270131 1KG_X_129270131 CACAG C . PASS . GT:GQ:BAF:LRR 0:0.499228:0.0:-0.0586095 +X 129519201 1KG_X_129519201 T TG . PASS . GT:GQ:BAF:LRR 0:0.377897:0.0:-0.345387 +X 130415294 1KG_X_130415294 T TG . PASS . GT:GQ:BAF:LRR 0:0.376958:0.0:0.0405394 X 134987551 newrs147659975 C T . PASS . GT:GQ:BAF:LRR .:0.0271973:0.855071529746:-1.02109 +X 134989190 1KG_X_134989190 GAGCT G . PASS . GT:GQ:BAF:LRR 0:0.387139:0.0:-0.05566 X 135095107 newrs149044510 C T . PASS . GT:GQ:BAF:LRR 0:0.517983:0.00356465578079:-0.024875 +X 135430860 1KG_X_135430860 T TG . PASS . GT:GQ:BAF:LRR 0:0.426777:0.0280655:-0.602415 +X 135741423 1KG_X_135741423 A AC . PASS . GT:GQ:BAF:LRR 0:0.361595:0.0:0.164597 +X 138820133 1KG_X_138820133 C CT . PASS . GT:GQ:BAF:LRR 0:0.500001:0.0:-0.0889456 +X 144904881 1KG_X_144904881 CT C . PASS . GT:GQ:BAF:LRR 0:0.748452:0.0:0.262683 +X 150912959 1KG_X_150912959 GAC G . PASS . GT:GQ:BAF:LRR 0:0.336045:0.0:0.0802203 X 152835147 newrs147874519 C T . PASS . GT:GQ:BAF:LRR 0:0.386838:0.0:0.0554279 X 153642450 newrs146934311 T C . PASS . GT:GQ:BAF:LRR 0:0.632201:0.0:-1.27112 X 153997508 newrs146700772 A C . PASS . GT:GQ:BAF:LRR 0:0.446295:0.0:-0.089962 diff --git a/tests/test_class.py b/tests/test_class.py index 80792f0..d0c20b1 100644 --- a/tests/test_class.py +++ b/tests/test_class.py @@ -81,7 +81,7 @@ def test(self): class RegressionIncludeAttributes(Regression): def test(self): output_vcf = tempfile.mktemp(suffix=".vcf") - command = [sys.executable, self.get_script(), "--genome-fasta-file", self.get_genome(), "--manifest-file", os.path.join(SCRIPT_DIR, "data", "small_manifest.bpm"), "--gtc-paths", os.path.join(SCRIPT_DIR, "data", "RegressionIncludeAttributes", "input", "201142750001_R01C01.gtc"), "--output-vcf-path", output_vcf, "--disable-genome-cache", "--skip-indels", "--include-attributes", "GT", "GQ", "BAF", "LRR"] + command = [sys.executable, self.get_script(), "--genome-fasta-file", self.get_genome(), "--manifest-file", os.path.join(SCRIPT_DIR, "data", "small_manifest.csv"), "--gtc-paths", os.path.join(SCRIPT_DIR, "data", "RegressionIncludeAttributes", "input", "201142750001_R01C01.gtc"), "--output-vcf-path", output_vcf, "--disable-genome-cache", "--include-attributes", "GT", "GQ", "BAF", "LRR"] self.run_regression(command, output_vcf, os.path.join(SCRIPT_DIR, "data", "RegressionIncludeAttributes", "output", "output.vcf")) os.remove(output_vcf) From c926e336c21084237533e67410bcf6f0e2b69ab5 Mon Sep 17 00:00:00 2001 From: Jake Zieve Date: Fri, 10 May 2019 13:58:53 -0700 Subject: [PATCH 29/34] Updates README to match field names in VCF --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 6dee2e1..a42d1e7 100644 --- a/README.md +++ b/README.md @@ -94,7 +94,7 @@ The GTC converter tool provides an option to supply a list of auxiliary records ### Include Attributes Default attributes to be included in the VCF are "GT" (genotype) and "GQ" (genotype score). With this option, you can compose which fields from the GTC are output to the VCF. -The additional fields available (from GTC version 5) are "BAF" (B-Allele Frequency) and "LRR" (Log-R Ratio). +The additional fields available (from GTC version 5) are "BAF" (B Allele Frequency) and "LRR" (Log R Ratio). ## Output description The VCF file output follows VCF4.1 format (https://samtools.github.io/hts-specs/VCFv4.1.pdf). Some additional details on output formatting: From 1f4e81bc55b254c1400e50329988db06039b01ef Mon Sep 17 00:00:00 2001 From: Jake Zieve Date: Tue, 14 May 2019 16:36:01 -0700 Subject: [PATCH 30/34] Fixes typo, better method naming --- BAlleleFreqFormat.py | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/BAlleleFreqFormat.py b/BAlleleFreqFormat.py index c2326e0..3181431 100644 --- a/BAlleleFreqFormat.py +++ b/BAlleleFreqFormat.py @@ -2,8 +2,7 @@ from IlluminaBeadArrayFiles import RefStrand import numpy as np -REVERSE_COMPLIMENT = {"A": "T", "T": "A", "G": "C", "C": "G", "I": "I", "D": "D"} - +REVERSE_COMPLEMENT = {"A": "T", "T": "A", "G": "C", "C": "G", "I": "I", "D": "D"} def extract_alleles_from_snp_string(snp_string): """ @@ -16,12 +15,12 @@ def extract_alleles_from_snp_string(snp_string): allele1 (string), allele2 (string) """ (allele1, allele2) = snp_string[1:4].split("/") - assert allele1 in "ATGCID", "allele %r is invalid (expected A,T,G,C,I,D)" % allele1 - assert allele2 in "ATGCID", "allele %r is invalid (expected A,T,G,C,I,D)" % allele2 + assert allele1 in REVERSE_COMPLEMENT, "allele %r is invalid (expected A,T,G,C,I,D)" % allele1 + assert allele2 in REVERSE_COMPLEMENT, "allele %r is invalid (expected A,T,G,C,I,D)" % allele2 return allele1, allele2 -def normalize_alleles_by_strand(snp_string): +def extract_reverse_complement_alleles_from_snp_string(snp_string): """ Splits SNP string into tuple of individual alleles and gets takes the reverse compliment to match strand 1 @@ -35,7 +34,7 @@ def normalize_alleles_by_strand(snp_string): # get alleles as tuple allele1, allele2 = extract_alleles_from_snp_string(snp_string) # get reverse compliment of bases and return - return REVERSE_COMPLIMENT[allele1], REVERSE_COMPLIMENT[allele2] + return REVERSE_COMPLEMENT[allele1], REVERSE_COMPLEMENT[allele2] def convert_indel_alleles(snp_string, vcf_record): @@ -107,9 +106,9 @@ def generate_sample_format_info(self, bpm_records, vcf_record, sample_name): # if indel, convert to actual ref and alt sequences if bpm_record.is_indel(): allele1, allele2 = convert_indel_alleles(snp, vcf_record) - # if 2/minus strand, normalize strand + # if 2/minus strand, get rev comp elif strand == RefStrand.Minus: - allele1, allele2 = normalize_alleles_by_strand(snp) + allele1, allele2 = extract_reverse_complement_alleles_from_snp_string(snp) else: allele1, allele2 = extract_alleles_from_snp_string(snp) From 3cb078af4bd2a986e1688cf93ac0d36bf82bac67 Mon Sep 17 00:00:00 2001 From: Jake Zieve Date: Tue, 14 May 2019 16:40:32 -0700 Subject: [PATCH 31/34] Fixes warnings related to file resources not getting closed --- tests/test_class.py | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/tests/test_class.py b/tests/test_class.py index d0c20b1..bd09b46 100644 --- a/tests/test_class.py +++ b/tests/test_class.py @@ -28,12 +28,13 @@ def run_regression(self, command, output, expected_output): def compare_vcf(self, output, expected_output): self.assertTrue(os.path.isfile(output)) - for (line1, line2) in zip(open(output), open(expected_output)): - if line1.startswith("##source") and line2.startswith("##source"): - continue - if line1.startswith("##reference") and line2.startswith("##reference"): - continue - self.assertEqual(line1, line2) + with open(output) as file1, open(expected_output) as file2: + for (line1, line2) in zip(file1, file2): + if line1.startswith("##source") and line2.startswith("##source"): + continue + if line1.startswith("##reference") and line2.startswith("##reference"): + continue + self.assertEqual(line1, line2) class RegressionBPM(Regression): def test(self): From d2940951df52a94a4da5e03c358854fa8a6f8990 Mon Sep 17 00:00:00 2001 From: Jake Zieve Date: Fri, 24 May 2019 14:22:14 -0700 Subject: [PATCH 32/34] Updated version to 1.2.0 --- gtc_to_vcf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gtc_to_vcf.py b/gtc_to_vcf.py index f95f3ab..643a5c0 100755 --- a/gtc_to_vcf.py +++ b/gtc_to_vcf.py @@ -17,7 +17,7 @@ from ReaderTemplateFactory import ReaderTemplateFactory from FormatFactory import FormatFactory -VERSION = "1.1.1" +VERSION = "1.2.0" def is_dir_writable(parent_dir): try: From 50f3920a53959ccad9b1f904c7ec18715838f5c4 Mon Sep 17 00:00:00 2001 From: Jake Zieve Date: Fri, 24 May 2019 14:36:24 -0700 Subject: [PATCH 33/34] Updates changelog for 1.2.0 --- changelog.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/changelog.md b/changelog.md index 0cee326..b649965 100644 --- a/changelog.md +++ b/changelog.md @@ -3,6 +3,12 @@ * Use chromosome ordering from reference * Use semi-colon as delimiter within identifier field +# 1.2.0 (2019/05/24) +* Fixes for python3 compatibility +* Fix for download_reference.sh to support more UNIX-y platforms +* Various small typos +* Support for outputting BAF and LRR + # 1.1.1 (2018/03/27) * Output warning if any mismatch to reference genome in indel source sequence * Count length of indel when scoring deletion reference allele From 8e2ee9802f8ae5b5eebc0c6d9b4ada9f392158ea Mon Sep 17 00:00:00 2001 From: KelleyRyanM Date: Fri, 24 May 2019 14:43:30 -0700 Subject: [PATCH 34/34] Move change log items from Development to 1.2.0 --- changelog.md | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/changelog.md b/changelog.md index b649965..db3c8a0 100644 --- a/changelog.md +++ b/changelog.md @@ -1,10 +1,7 @@ -# Development -* Python3 compatibility fixes -* Use chromosome ordering from reference -* Use semi-colon as delimiter within identifier field - # 1.2.0 (2019/05/24) * Fixes for python3 compatibility +* Use chromosome ordering from reference +* Use semi-colon as delimiter within identifier field * Fix for download_reference.sh to support more UNIX-y platforms * Various small typos * Support for outputting BAF and LRR @@ -23,4 +20,4 @@ * Eliminated extraneous header in column # 1.0.0 (2017/10/15) -* Initial release \ No newline at end of file +* Initial release