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konradjk / exac_browser

Browser for ExAC consortium data
http://exac.broadinstitute.org
MIT License
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chr X Allele Numbers #276

Open annblackz opened 8 years ago

annblackz commented 8 years ago

Good morning,

We noticed that the allele numbers for SNPs in chrX do not appear to take account of the gender of the sample. I was assuming the maximum AN would be 2(Number of Female Samples) + (Number of Male Samples). Instead, it appears to be 2 (Number of total samples).

For example:

http://exac.broadinstitute.org/variant/X-155235086-T-C

I was hoping someone might be able to provide some additional information as to how AN for chr X in ExAC data should be used?

Thanks so much,

Ann Black-Ziegelbein

rjsicko commented 6 years ago

this may have changed from when you posted this question, but I believe the AC now takes into account male and female samples.

Your example is in the PAR#2

See another example: http://exac.broadinstitute.org/variant/X-70328185-C-T

which has 86,817 allleles.

annblackz commented 6 years ago

Thank you, yes - I posted my original question in 2016.

Ann

On Fri, Feb 9, 2018 at 11:50 AM Robert Sicko notifications@github.com wrote:

this may have changed from when you posted this question, but I believe the AC now takes into account male and female samples.

Your example is in the PAR#2 https://www.ncbi.nlm.nih.gov/grc/human

See another example: http://exac.broadinstitute.org/variant/X-70328185-C-T

which has 86,817 allleles.

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