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