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szpiech / selscan

Haplotype based scans for selection
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XPEHH Results #114

Open tori-rudolph opened 1 month ago

tori-rudolph commented 1 month ago

Hello,

I am using selscan XPEHH to compare males and females of a given population. I noticed in the males there is a long run of heterozygosity on chromosome 15, while females have homozygosity. I have included below the genotypes from my vcf file for the males and females at 2 SNPs below. When I normalize and plot the data this region does not come up as under selection in the females compared to males. Could you explain how this could be? My sample sizes are pretty small, 10 females and 15 males. Males: 15 30283568 15:30283568 G A . . PR;AC=14;AN=30 GT 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 15 30283949 15:30283949 C A . . PR;AC=14;AN=30 GT 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 Females: 15 30283568 15:30283568 G A . . PR;AC=0;AN=20 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 15 30283949 15:30283949 C A . . PR;AC=0;AN=20 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0

Any insight would be greatly appreciated!

szpiech commented 1 month ago

Hello,

Well, this is only two sites and the statistic looks for extended regions of homozygosity in one group vs the other. If these are the only sites showing this pattern, then I’m not surprised there is no conspicuous signal from the statistic.

Zachary

Le mar. 21 mai 2024 à 15:51, tori-rudolph @.***> a écrit :

Hello,

I am using selscan XPEHH to compare males and females of a given population. I noticed in the males there is a long run of heterozygosity on chromosome 15, while females have homozygosity. I have included below the genotypes from my vcf file for the males and females at 2 SNPs below. When I normalize and plot the data this region does not come up as under selection in the females compared to males. Could you explain how this could be? My sample sizes are pretty small, 10 females and 15 males. Males: 15 30283568 15:30283568 G A . . PR;AC=14;AN=30 GT 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 15 30283949 15:30283949 C A . . PR;AC=14;AN=30 GT 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 Females: 15 30283568 15:30283568 G A . . PR;AC=0;AN=20 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 15 30283949 15:30283949 C A . . PR;AC=0;AN=20 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0

Any insight would be greatly appreciated!

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tori-rudolph commented 1 month ago

Hi Zachary,

I looked at the vcf files to get a better idea of how big this region is and it stretches about 18 kb

szpiech commented 1 month ago

Honestly, I do not have enough information to explain why you don’t see the pattern you expect. I have very little to go on as it is. I’m currently on parental leave. Perhaps later in the summer you can give me more details, and I can try to help more then.

Zachary

Le mer. 22 mai 2024 à 15:15, tori-rudolph @.***> a écrit :

Hi Zachary,

I looked at the vcf files to get a better idea of how big this region is and it stretches about 18 kb

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