SEQ description

[brobr]

Hi, thanks for the concise overview of a sam file but I am struggling with some of the descriptors. Like the one for SEQ, in the spec on www.htslib.org/doc/sam.html described as

10 | SEQ | query SEQuence on the same strand as the reference

which could be ambiguous when it is not known what strand of the reference has been used (upper, lower, both?) for the aligning.

In the intro on this site SEQ is described to be "the raw sequence" as found in the fastq file:

Finally, you have the data from the original FASTQ file stored for each read. That is the raw sequence (SEQ) ...

But does the SEQ not give the sequence present in the fasta file used as the reference for aligning, which is normally the sense strand? Not the raw sequence. This difference is important when the mapped raw read has been on the reverse (antisense) strand, which is annotated in the flag with 16.

Thus, for mapped reads antisense to the reference would one not expect the reverse compliment sequence as SEQ (and thus not the raw fastq sequence)?