3K Grouping

This tool is based on population structure of 3K rice genomes, which is classified by ADMIXTURE for K=9.

Submit your sample list (one sample per line):
- Hide 3K group (3024 samples) Download 3K group file
K9 Group Group Size Description
XI-1A 209 Xian/indica subpopulation 1A
XI-1B 205 Xian/indica subpopulation 1B
XI-2 285 Xian/indica subpopulation 2
XI-3 475 Xian/indica subpopulation 3
XI-adm 615 Xian/indica admixed types between two or more XI subpopulations
GJ-adm 82 Geng/japonica admixed types between two or more GJsubpopulations
GJ-trp 372 Geng/japonica tropical subpopulation
GJ-sbtrp 113 Geng/japonica subtropical subpopulation
GJ-tmp 287 Geng/japonica temperate subpopulation
cA(Aus) 201 centrum-Aus population
cB(Bas) 76 centrum-Basmati population
admix 103 admixed between any two or more of the XI, GJ, cA (Aus), cB (Bas) populations
The population structure of the 3K-RG dataset was analysed using ADMIXTURE software on the core SNP set (version 0.4).
First, ADMIXTURE was run on 30 random 100,000-SNP subsets of the core SNP set with k (the number of groups) ranging from 5 to 18, and k = 9 was chosen because it was the minimal value of k to separate all previously known groups (cA, cB, XI, GJ-trp, GJ-tmp and part of GJ-sbtrp).
With k = 9, ADMIXTURE was then run again on the whole core SNP set nine times with varying random seeds; the Q-matrices were aligned using CLUMPP software and clustered on the basis of similarity.
Then, the matrices belonging to the largest cluster were averaged to produce the final matrix of admixture proportions.
Finally, the group membership for each sample was defined by applying the threshold of ≥ 0.65 to this matrix. Samples with admixture components <0.65 were classified as follows. If the sum of components for subpopulations within the major groups XI and GJ was ≥ 0.65, the samples were classified as XI-adm or GJ-adm, respectively, and the remaining samples were deemed 'fully' admixed (admix).
The phylogenetic tree is displayed below, branches of which are coloured according to the K9 classification.