confusion on the results of hapmers.sh

[leon945945]

Following the advice of marbl/meryl#53 (comment), I tried hapmers.sh of merqury, and I got the following results:

KmerType FolderSize
maternal.inherited.meryl/ 3.5Gb
paternal.inherited.meryl/ 2.8Gb
shrd.inherited.meryl/ 1.1Gb
read.only.meryl/ 14Gb

According to the folder size of results, the read-only-kmers account a large proportion of progeny's kmers. Which means the origin of these DNA sequences are unknown.
In my opinion, the DNA of progeny should be inherited from mat or pat, why there exists a large proportion of unknown DNA sequences, and what is the probable reason?
Very hope for your reply. Thanks very much.

[arangrhie]

Hi @leon945945 ,

glad you are trying the hapmer script! Do you have the plot handy? Or the final .hist file?

[leon945945]

Hi @arangrhie ,

I get the final plot, I'm not clear with each filled region in the plot, and I want to understand why the read-only-kmers account for a large proportion. Looking forward to your reply.