1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
|
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
|
