plink软件计算基因频率产生NA的原因

 

001、

root@PC1:/home/test# ls
outcome.map  outcome.ped
root@PC1:/home/test# cat outcome.map          ## 测试数据map文件
20      OAR20_27119.1   0       217914
20      OAR20_192404.1  0       308307
21      OAR21_338481.1  0       230847
21      OAR21_369726.1  0       262607
22      OAR22_728735.1  0       260996
22      OAR22_832781.1  0       363750
23      OAR23_393569_X.1        0       299533
23      OAR23_429075.1  0       335259
24      s75016.1        0       56233
24      s72739.1        0       96354
25      s33329.1        0       83221
25      DU455254_479.1  0       100959
26      OAR26_222715_X.1        0       165273
26      OAR26_291834.1  0       205049
root@PC1:/home/test# plink --file outcome --freq --out result &>/dev/null; rm *.log *.nosex
root@PC1:/home/test# ls
outcome.map  outcome.ped  result.frq
root@PC1:/home/test# cat result.frq        ## 查看结果
 CHR                SNP   A1   A2          MAF  NCHROBS
  20      OAR20_27119.1    A    C        0.125      880
  20     OAR20_192404.1    G    A       0.3057      880
  21     OAR21_338481.1    A    G          0.4      880
  21     OAR21_369726.1    C    A       0.4148      880
  22     OAR22_728735.1    C    A      0.09432      880
  22     OAR22_832781.1    A    G       0.4057      880
  23   OAR23_393569_X.1    A    G       0.4068      880
  23     OAR23_429075.1    G    A       0.3011      880
  24           s75016.1    0    C           NA        0
  24           s72739.1    G    A           NA        0
  25           s33329.1    A    G        0.167      880
  25     DU455254_479.1    A    G       0.1602      880
  26   OAR26_222715_X.1    A    G       0.4614      880
  26     OAR26_291834.1    G    A       0.2795      880

 

产生NA的原因在于计算物种的染色体数目有24； 24号染色体的数据， plink计算默认全部生成为NA。