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 mr1242 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
vg0421387824 sf0421215877 4 21387824 4.05E-17 9.03E-11
vg0108582948 sf0108581948 1 8582948 2.24E-15 2.83E-09
vg0700863821 sf0700862821 7 863821 4.52E-13 4.15E-08
vg0504875404 sf0504875381 5 4875404 1.51E-12 4.69E-07
vg1219134304 sf1219105740 12 19134304 4.27E-12 7.00E-08
vg1014514985 sf1014443751 10 14514985 6.23E-11 3.16E-07
vg0200923972 sf0200923972 2 923972 1.34E-10 2.17E-07
vg1002009944 sf1002008921 10 2009944 1.88E-10 1.37E-07
vg0336193973 sf0336186899 3 36193973 2.01E-10 1.34E-07
vg1004727190 sf1004743727 10 4727190 2.68E-10 2.84E-07
vg0910545581 sf0910544580 9 10545581 1.69E-09 4.83E-08
vg0136191693 sf0136190650 1 36191693 2.18E-09 3.80E-07
vg0625443240 sf0625442243 6 25443240 2.65E-09 4.13E-07
vg1117137503 sf1116671355 11 17137503 1.51E-08 7.25E-08
vg0405896767 sf0405892208 4 5896767 2.57E-08 2.84E-07
vg0112321732 sf0112320706 1 12321732 3.66E-08 2.38E-07
vg0432345183 sf0432160072 4 32345183 5.17E-08 1.27E-08
vg0102531039 sf0102530039 1 2531039 1.26E-07 2.16E-06
vg0224215161 sf0224209292 2 24215161 5.97E-07 2.33E-08
vg0133772255 sf0133771211 1 33772255 2.38E-06 4.67E-07
vg0225318037 sf0225312168 2 25318037 4.65E-06 NA
vg0221025908 sf0221020040 2 21025908 7.12E-06 2.09E-07
vg0804875587 sf0804874590 8 4875587 NA 1.19E-07