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XPEHH Results #114
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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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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 |
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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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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