BAM file sequence homology between individual WGS of same species

Question

[rtyb91]

Dear all,

I am currently analyzing WGS sequencing of dogs and my primary investigator is always pondering about the sequence homology percentage of the data among each dogs.

For examples, we have been told the genome of human and dogs are at about 70%, and he wishes to know how similar are the reads/sequences of the data between the dogs we have sequenced.

I am wondering if we can do that with BAM files from the reads aligned to the reference to product percentage similarity/homology/identity between the samples we have sequenced.

My WGS samples are sequenced using Illumina NOVAseq6000 and MGI DNBSeq

Thank you.

[GenoMax]

I am wondering if we can do that with BAM files from the reads aligned to the reference to product percentage similarity/homology/identity between the samples we have sequenced.

When you are looking at overall stats like X% alignment to a reference genome for one sample and Y% for a second sample to the same reference you would not be able to say anything about relatedness of the two samples to each other by just looking at those alignment percentages.

[rtyb91]

In that case, what would be the best way to say something about the relatedness between samples? Would that be sequence homology only?