Why some markers can be genotyped on chromosome y in female samples
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0
Entering edit mode
7.8 years ago
ShirleyDai ▴ 50

Hi, I used plink to clean my dataset. All sample in the dataset were believed female. But I can see some marker on Chr24 do exit in female samples. How this happens?
thanks!

head OC_sex.map
24      rs11575897      0       2655180
24      rs2534636       0       2657176
24      200610-249      0       2658869
24      rs35840667      0       2661306
24      200610-252      0       2661836
24      rs35067692      0       2663685
24      rs9786608       0       2663943
24      rs2058276       0       2668456
24      rs13303871      0       2679100
24      rs11799203      0       2705854

less -S OC_sex.ped
1       TB5943  0       0       2       2       0 0     0 0     0 0     0 0     0 0     0 0     G G     0 0     G G     0 0     0 0     0 0     G G     0 0     0 0     0 0     0
1       TB5459  0       0       2       2       0 0     0 0     0 0     0 0     0 0     0 0     G G     0 0     G G     0 0     0 0     0 0     G G     0 0     0 0     0 0     0
1       TB1000231       0       0       2       2       0 0     0 0     0 0     0 0     0 0     0 0     G G     0 0     G G     G A     G G     0 0     G G     0 0     0 0     0
1       62      0       0       2       2       0 0     0 0     0 0     0 0     0 0     0 0     G G     0 0     G G     0 0     0 0     0 0     G G     0 0     0 0     0 0     0
1       100     0       0       2       2       0 0     0 0     0 0     0 0     0 0     0 0     G G     0 0     G G     0 0     0 0     0 0     G G     0 0     0 0     0 0     0
1       TB854   0       0       2       2       0 0     0 0     0 0     0 0     0 0     0 0     G G     0 0     G G     G A     0 0     0 0     G G     0 0     0 0     0 0     0
1       TB2853  0       0       2       2       0 0     0 0     0 0     0 0     0 0     0 0     G G     0 0     G G     0 0     0 0     0 0     G G     0 0     0 0     0 0     0
1       TB4777  0       0       2       2       0 0     0 0     0 0     0 0     0 0     0 0     G G     0 0     G G     0 0     0 0     0 0     G G     0 0     0 0     0 0     0
1       TB-896  0       0       2       2       0 0     0 0     0 0     0 0     0 0     0 0     G G     0 0     G G     0 0     0 0     0 0     G G     C A     0 0     0 0     0
1       TB-1048 0       0       2       2       0 0     0 0     0 0     C A     G A     C A     G G     0 0     G G     G A     0 0     0 0     G G     0 0     0 0     0 0     0
1       TB-1051 0       0       2       2       0 0     0 0     0 0     C A     0 0     0 0     G G     0 0     G G     G A     G G     0 0     G G     0 0     G A     0 0     0
plink gwas • 2.1k views
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1
Entering edit mode

What is your genotyping platform? Did you run imputation? Some of the markers might be located in regions that are similar enough to give a signal, based on the short probes on genotyping arrays; there aare some regions with DNA sequence similarity between X and Y. If you know your sample is female, you should filter the markers on Y.

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0
Entering edit mode

My platform is Illumina.This data have not been imputed. I think your answer is reasonable. Thanks

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