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smartpca output description #31

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nottwy opened this issue Sep 5, 2018 · 0 comments
Open

smartpca output description #31

nottwy opened this issue Sep 5, 2018 · 0 comments

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@nottwy
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nottwy commented Sep 5, 2018

I'm trying to get as much useful information as I can. But I find that there is rare information about the output of smartpca.
Could you please explain these sectors?
1.
kurtosis snps indivs
eigenvector 1 19.748 8.548
eigenvector 2 10.372 1.793
eigenvector 3 11.369 2.928
eigenvector 4 14.368 5.535
eigenvector 5 14.923 5.712
eigenvector 6 11.614 2.647

eigbestsnp 1 NW_005392842.1_342309 1 3475 7.095
eigbestsnp 1 NW_005392842.1_1092099 1 3629 7.095
eigbestsnp 1 NW_005392842.1_1092105 1 3630 7.095
eigbestsnp 1 NW_005392858.1_844626 1 7110 7.095
eigbestsnp 1 NW_005392858.1_917105 1 7157 7.095
eigbestsnp 1 NW_005392858.1_1019387 1 7194 7.095
eigbestsnp 1 NW_005392872.1_2150841 1 9626 7.095

total number of snps killed in pass: 504962 used: 199335

number of samples used: 15 number of snps used: 704297

nodata: NW_005404811.1_267
nodata: NW_005404830.1_2218

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