QC for GorGor

[andrewkern]

QCing the species addition for GorGor #1517

this pertains to issue #1659 as well

I've gone through and everything looks good except for the mutation rates initially drafted by @ChristianHuber

The mutation rate estimate in the catalog currently is 1.235e-08. Looking at the citation I see that they sequenced two gorilla trios, one of which had a rate of 1.03e-08 and the other which was at 1.22e-08. Averaging these I came up with a rate of 1.125e-08.

@ChristianHuber -- do you see different numbers reported?

[andrewkern]

Also for recombination rates, I see that chromosome X was given the genome average rate (which we agree on) but no data in the citation was given about X-linked recombination rates. In my QC PR I've set it to zero, so this will fail tests. I'm not sure as to the best way to proceed here. Perhaps @petrelharp has an opinion of what to do in this case?

[petrelharp]

Lacking other information, we set the rate on the X to the autosomal rate, I'd say - pretty sure this is what we do elsewhere, and this will be closer to correct than 0.

[petrelharp]

I know what it is! Those two reported mutation rates are for particular gorillas with particular parental ages; they've then used assumptions about how the mutation rate varies with age to extrapolate to an average mutation rate across time. They report 0.65e-9 mutations/year and a generation time of 19 years (as in the catalog); and 1.235e-8 = 0.65e-9 * 19.

This seems pretty reasonable to me, FWIW. (Clearly, though, the calculation should be documented.)

[petrelharp]

LGTM except for issues discussed

[andrewkern]

Nice! So I'll make these changes on the QC and we should be good to go here

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.85%. Comparing base (9008882) to head (8d7d9b0).
Report is 1 commits behind head on main.

Additional details and impacted files

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##             main    #1701   +/-   ##
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  Coverage   99.85%   99.85%           
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  Files         139      139           
  Lines        4851     4851           
  Branches      470      470           
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  Hits         4844     4844           
  Misses          3        3           
  Partials        4        4           

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