Question: Reference TiTv ratio for mouse WGS?
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gravatar for serpalma.v
10 weeks ago by
serpalma.v20
Germany
serpalma.v20 wrote:

Hello!

I am wondering if anyone has a reference for the Ti Tv ratio in mouse WGS.

I've gone through the literature but without much success except two publications. This publication calculates the TiTv ratio for het-SNPs (Ti=66.3%; Tv=33.7%) and hom-SNPs (Ti=77.7%; Tv=22.3%), which I interepreted as 1.96 for het-sites and 3.48 for hom-sites. Keep in mind that they did not use all chromosomes for this calculation. This other publication sequenced the whole genome of two mice of different strains and reports the TITv ratio only for the strain-specific set of SNPs (1.5 and 1.7).

Also I run Picard's CollectVariantCallingMetrics on the variants reported by the Mouse Genomes Project (v5) and foud the following:

| DBSNP_TITV| NOVEL_TITV|
|----------:|----------:|
|   2.078266|   1.812511|

And in my own data (60 samples, WGS, ~20x) I see something similar

| DBSNP_TITV| NOVEL_TITV|
|----------:|----------:|
|   2.122095|   1.664997|

My questions are the following:

  • Is there a study I am missing that indicates the expected TiTv for mouse?
  • Could I just take the Mouse Genomes Project TiTv ratio as my reference and conclude that the TiTv ratio I observe in my data is acceptable?

Thanks in advance!

ADD COMMENTlink modified 14 days ago by Biostar ♦♦ 20 • written 10 weeks ago by serpalma.v20
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