Why some markers can be genotyped on chromosome y in female samples
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
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ShirleyDai •
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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.
My platform is Illumina.This data have not been imputed. I think your answer is reasonable. Thanks