Number of variants from mouse exome looks very small

[Shingo]

Hello everybody,

I’m just starting to analyze mouse exome. I got mouse exome fastq files (SRR519332) looks like Agilent SureSelect mouse all exon v1 from DRA/SRA/ERA.

http://trace.ddbj.nig.ac.jp/DRASearch/experiment?acc=SRX158290

Using the exome target file (S0276129_Covered.bed, 50Mb) from Agilent SureDesign, I called SNP/InDel by GATK 1.6 and AvadisNGS 1.4.6. Both of programs yielded about 6,000 variants and matching rate was about 80%. Average read depth of coverage on the target region was about 70 by GATK’s DepthOfCoverage.

Is the number of variants reasonable?

When I analyzed human exome (SureSelect All human 50Mb) I got about 50,000 variants. The number of variants from mouse exome looks very small compare than human.

Thank you.

[Bukowski]

Mice are generally inbred strains, so there is much less genetic variation than in a human population. Consequently you might expect less variants.

[Shingo]

Thank you for the reply. I understood the reason. I'm worried I had something mistake.