Question: How come female has variants in chrY and How come male variants in chrX are represented as two alleles?
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gravatar for genomicsngs2017
15 months ago by
genomicsngs20170 wrote:

Hi Friends,

I am a new user to NGS arena. I pasted a couple of vcf records for chrY and chrX from trio analysis.

1) Genotype (GT) for son is 0/1, which is heterozygous. 0 refers to the reference allele and 1 refers to the alternate allele. We get one chromosome from each parent. One parent's chromosome has 0 (same as reference allele) and another parent's chromosome has 1 (different from reference allele).

2) Same with father's genotype

3) Genotype for mother is 1/1, which is homozygous alternate. 1 refers to the alternate allele. So both the parent's chromosome have 1 (different from reference allele).

Is my understanding about the genotype correct?

4) Allele Count - AC : 1 alternate allele from son, 2 alternate alleles from mother and 1 alternate allele from father, so total four(4) alternate alleles. Therefore AC refers to alternate allele count.

5) Total Allele - AN : 2 alleles for son, 2 alleles for mother and 2 alleles for father, so total 6 alleles.

6) Allele Frequency AF: 4/6 is 0.667. So this allele frequency refers alternate allele frequency. Am I correct?

Female doesn't have chromosome Y, so the genotype in chromsome Y should be like this right "nil" ,but how come the mother sample has 1/1 genotype in chrY?

enter image description here

Similarly, for the variants in chrX,

Only mother should have two X chromosomes, so she has 1/1 logically correct. But how come son and father also having 1/1 (two alleles), because male has only one X chromsome that should be represented as "1(one allele)". I am confused about it. enter image description here

ADD COMMENTlink modified 15 months ago • written 15 months ago by genomicsngs20170
1

some variant callers have no idea of what is a sexual chromosome: e.g: http://gatkforums.broadinstitute.org/gatk/discussion/5228/

ADD REPLYlink written 15 months ago by Pierre Lindenbaum110k

Thanks Pierre for the link. I read it.

Do they mean, the variants called in chromosome X and Y are not confident calls because of their depth?

How to people calls variants for sex related inherited disease?

ADD REPLYlink written 15 months ago by genomicsngs20170

Hi, Don't know if it help but yes you can check metric as depth coverage and frequencies of variation. The think is eliminate sequencing errors and align errors. There are 2 possibilities for me : - You got contamination during sequencing or library making - Your sequences are on chr X and Y are not specific of the position and can be aligned on other chromosome

Best

ADD REPLYlink written 15 months ago by Titus610
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