Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1855 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0431803015 sf0431617908 4 31803015 5.24E-14 5.24E-14
vg0910545581 sf0910544580 9 10545581 3.93E-12 3.93E-12
vg1124422531 sf1123956371 11 24422531 1.34E-09 1.34E-09
vg0820198596 sf0820195883 8 20198596 2.01E-09 2.01E-09
vg1123222536 sf1122756407 11 23222536 3.44E-09 3.44E-09
vg0124141412 sf0124140368 1 24141412 3.54E-09 3.54E-09
vg0712987215 sf0712986222 7 12987215 5.03E-09 5.03E-09
vg1124474136 sf1124007976 11 24474136 8.30E-09 8.30E-09
vg1003806408 sf1003805384 10 3806408 2.78E-08 2.78E-08
vg0225485692 sf0225479823 2 25485692 4.43E-08 4.43E-08
vg0518025487 sf0517964973 5 18025487 7.53E-08 7.53E-08
vg0618508336 sf0618507339 6 18508336 8.45E-08 8.45E-08
vg0315349538 sf0315348185 3 15349538 1.20E-07 1.20E-07
vg1220059260 sf1220030702 12 20059260 1.30E-07 1.30E-07
vg0114364662 sf0114363636 1 14364662 1.31E-07 1.31E-07
vg0711050248 sf0711049254 7 11050248 2.24E-07 2.24E-07
vg0521569979 sf0521507420 5 21569979 3.17E-07 3.17E-07
vg1121318047 sf1120851925 11 21318047 4.82E-07 4.82E-07
vg0430105040 sf0429919911 4 30105040 7.91E-07 7.91E-07
vg0203441067 sf0203441065 2 3441067 9.64E-07 9.64E-07