Diploid calls on chrY?

Hello,

I recently got my genome sequenced.

chrY    59030922    .   A   G   1244.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-6.580e-01;ClippingRankSum=0.00;DP=41;ExcessHet=3.0103;FS=9.230;MLEAC=1;MLEAF=0.500;MQ=37.33;MQRankSum=-4.563e+00;QD=30.36;ReadPosRankSum=-7.570e-01;SOR=0.076;VQSLOD=0.452;culprit=FS  GT:AD:DP:GQ:PL  0/1:9,32:41:99:1273,0,180 
chrY    59032665    .   A   G   418.77  PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-4.182e+00;ClippingRankSum=0.00;DP=52;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=45.59;MQRankSum=-6.082e+00;QD=8.21;ReadPosRankSum=-1.528e+00;SOR=0.756;VQSLOD=2.78;culprit=DP    GT:AD:DP:GQ:PL  0/1:25,26:51:99:447,0,492

the key part is that I see diploid calls "0/1" for the GT field.

Why am I seeing these? Shouldn't chrY be haploid? or is this XYY syndrome?

genome vcf

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updated 7.5 years ago by finswimmer

• written 7.5 years ago by dec986

Big chunks of Y are copied on X, so maybe this is the so-called pseudo-autosomal region?

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written 7.5 years ago by karl.stamm

1 answer

Some regions of chrY are duplicated on chrX, it's called the pseudo-autosomal region, because it appears to behave like autosomes.

Wikipedia tells me that this location, 59megabases could be included .

https://en.wikipedia.org/wiki/Pseudoautosomal_region

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written 7.5 years ago by karl.stamm

thank you! that is very useful. All 2,796 of my sites are diploid, from 2,649,476 to 59,032,665 Is there a possibility of some sort of technical error, or is this genuine XYY?

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written 7.5 years ago by dec986

As far as I know in the case of XYY your Y chromosomes would be identical.

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written 7.5 years ago by WouterDeCoster

I was thinking about it, how to have 2 différent Y chromosomes? If your father already have a XYY, you could have a de novo mutation… the avarate rate of of this are 5 mutations per generation for the whole genome… meaning the chance one occurred on a Y is low, and it is a single base. So per sequencing, error rates is bigger…

To get 2 different Y, you need your mother having XY and an issue (such as sry missing Y) making her female. Then a ségrégation error with an ovocyte XY, fertilised with a sperm carrying Y… Should be as rare as a male calico cat with klinefelter syndrome

Anyway, the best way to know if you are XYY (pretty common actually) is to get a caryotype.

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written 7.5 years ago by gbl1

These are the reference and alternate allele frequencies (count, and then GT within VCF):

  2511 0/1
    280 1/1
      5 1/2

I don't know what to think anymore

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written 7.5 years ago by dec986