Tau values

Tau Values:

tau values much less than 100 need investigating. Ex:
tau (African)   242.128
tau (European)   187.366
 

Hardy Weinberg check:

Scores above 3.5 are dubious, and above 4 a problem. Ex:
hwcheck            rs2041809   2  619     6.250
*** this is probably bad.
hwcheck            rs2051772  11 3008     3.240
hwcheck            rs7917364  10 2835     2.603

Mapcheck:

Scores above 3 dubious. Ex:
mapcheck            rs2249265   289     0.088
mapcheck           rs11466112   226     0.012
Everything looks OK  

Freqcheck

freqcheck all: The output from freqcheck is sorted by the S(All) column, ex:
freqcheck            rs2356419    23    40.821    20.446     0.367     0.422       0.473     0.670
freqcheck            rs3911730    18    26.302    17.775     0.009     0.994       0.004     1.000
freqcheck           rs12662847     6    23.947    11.011     0.457     0.960       0.377     1.000
freqcheck            rs2453042     1    22.537    11.679     0.983     0.010       0.989     0.000
freqcheck            rs1493695     1    21.345    16.188     0.006     0.972       0.000     0.994
freqcheck            rs2493410     1    20.978    13.633     0.003     0.992       0.000     1.000
freqcheck           rs10871664    18    20.027     7.923     0.988     0.012       0.994     0.006
freqcheck             rs947273     1    17.861    10.791     0.066     0.985       0.061     0.999
freqcheck             rs699780     1    14.469     7.164     0.044     0.971       0.055     0.976
freqcheck             rs896999    15     9.637     7.313     0.263     0.985       0.261     1.000
All these except the last are doubtful,  the top few impossible.

freqcheck controls : The output from freqcheck is sorted by the S(Controls) column, ex:
freqcheck            rs2356419    23    40.821    20.446     0.367     0.422       0.473     0.670
freqcheck            rs3911730    18    26.302    17.775     0.009     0.994       0.004     1.000
freqcheck            rs1493695     1    21.345    16.188     0.006     0.972       0.000     0.994
freqcheck            rs2493410     1    20.978    13.633     0.003     0.992       0.000     1.000
freqcheck            rs2453042     1    22.537    11.679     0.983     0.010       0.989     0.000
freqcheck           rs12662847     6    23.947    11.011     0.457     0.960       0.377     1.000
freqcheck             rs947273     1    17.861    10.791     0.066     0.985       0.061     0.999
freqcheck             rs798058     1     0.282    10.628     0.166     0.447       0.228     0.610
freqcheck             rs699738     1     2.437     8.491     0.688     0.050       0.681     0.017
freqcheck            rs1557519    16     4.177     8.481     0.061     0.955       0.054     0.982
Only rs798058 shows anything new here (not caught by all).  I'd probably delete it.

checkindiv

checkindiv         toyindiv:865     0.446   103.965     5.699 2178   1939.409    0.890

checkindiv        toyindiv:1076     0.522    62.293     3.478 2178   2064.101    0.948

checkindiv        toyindiv:1109     0.490    61.938     3.452 2178   2048.490    0.941

checkindiv         toyindiv:559     0.433    55.725     3.030 2178   1966.424    0.903

checkindiv         toyindiv:968     0.504    53.800     3.004 2178   2096.531    0.963

checkindiv          toyindiv:83     0.420   -61.425    -3.311 2178   2290.904    1.052

checkindiv         toyindiv:799     0.224   -86.671    -3.706 2178   2828.520    1.299

checkindiv         toyindiv:397     0.339   -96.007    -4.782 2178   2585.970    1.187

They look fine