Skip to content

cropevolution/PopAmaranth

 
 

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

39 Commits
 
 
 
 
 
 
 
 
 
 

Repository files navigation

Project Overview

Gene annotation:

200,797 total number of genes 23,884 have annotation

General summary statistics:

Raisd analysis:

species total sites detected sites>1% threshold nr windows cut-off
caudatus 1765126 17650 973 4.111e-05
cruentus 1654914 16546 1096 5.345e-05
hypochondriacus 1793173 17932 1121 5.33828e-05
hybridus 4343653 43415 2452 2.269e-05
quitensis 1585410 15854 1275 9.241e-05

number of sites (saf files)

species total sites
caudatus 331601031
cruentus 332584629
hypochondriacus 363428489
hybridus 259369182
quitensis 347013541

number of SNPs

species total sites
caudatus 4961210
cruentus 4075368
hypochondriacus 4551278
hybridus 12238589
quitensis 2342505

FST values

species mean Fst Value
caudatus/cruentus 0.681
caudatus/hybridus 0.325
caudatus/hypochondriacus 0.619
caudatus/quitensis 0.172
cruentus/hybridus 0.688
cruentus/hypochondriacus 0.572
cruentus/quitensis 0.730
hybridus/quitensis 0.348
hypochondriacus/hybridus 0.329
hypochondriacus/quitensis 0.676

sweeps

average window size
caudatus 36055.6
cruentus 41195.1
hypochondriacus 42156.5
hybridus 30257.5
quitensis 41940.9

0.5740122571295846

inbreeding coefficient

mean value
caudatus 0.574
cruentus 0.488
hypochondriacus 0.628
hybridus 0.677
quitensis 0.189

Tajima's D

mean value
caudatus 1.443
cruentus 1.773
hypochondriacus -0.105
hybridus -0.597
quitensis 2.037

nucleotide diversity (π)

mean value
caudatus 0.009
cruentus 0.010
hypochondriacus 0.005
hybridus 0.019
quitensis 0.009

Wu and Watterson estimator (θ)

mean value
caudatus 0.007
cruentus 0.007
hypochondriacus 0.005
hybridus 0.023
quitensis 0.006

beagle file (all samples)

116 samples 388751022 sites

About

No description, website, or topics provided.

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages

  • HTML 99.9%
  • Other 0.1%