parameter file: par.example
### THE INPUT PARAMETERS
##PARAMETER NAME: VALUE
genotypename: ../CONVERTF/example.ped
snpname: ../CONVERTF/example.map
indivname: ../CONVERTF/example.ped
evecoutname: example.evec
evaloutname: example.eval
altnormstyle: NO
numoutevec: 2
familynames: NO
grmoutname: grmjunk
## smartpca version: 13050
norm used

genotype file processed
number of samples used: 5 number of snps used: 7
Using 2 threads, and partial sum lookup algorithm.
total number of snps killed in pass: 0  used: 7
grm dumped

## To get Tracy-Widom statistics: recompile smartpca with TWTAB correctly specified in Makefile, or
   just run twstats (see README file in POPGEN directory)
    kurtosis           snps    indivs
 eigenvector    1     1.271     1.505
 eigenvector    2     1.796     2.127
population:   0                 Case    2
population:   1              Control    3

## Average divergence between populations:
                 Case    Control     popsize
      Case      0.849      3.298           2
   Control      3.298      1.151           3


number of blocks for moving block jackknife: 1
fst *1000:
          C     C 
   C      0     0
   C      0     0

s.dev * 1000000:
          C     C 
   C      0     0
   C      0     0

eigenvector 1:means
             Control     -0.336
                Case      0.505
## Anova statistics for population differences along each eigenvector:
                                              p-value
             eigenvector_1_Case_Control_     0.0262738 
eigenvector 2:means
             Control     -0.056
                Case      0.084
             eigenvector_2_Case_Control_      0.805663 

## Statistical significance of differences beween populations:
                                pop1                  pop2      chisq          p-value   |pop1|   |pop2|
popdifference:                  Case               Control         9.554    0.00842201       2       3

##end of smartpca run
