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 mr1395 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
vg0618618072 sf0618617075 6 18618072 5.00E-11 1.57E-09
vg0406995300 sf0406990571 4 6995300 9.39E-11 3.18E-08
vg0615249109 sf0615248110 6 15249109 1.11E-10 6.33E-06
vg0615245465 sf0615244466 6 15245465 5.44E-10 4.37E-07
vg1218763524 sf1218734959 12 18763524 1.83E-09 8.87E-10
vg0406592386 sf0406587830 4 6592386 3.45E-09 1.32E-06
vg0410250947 sf0410241644 4 10250947 9.74E-09 1.48E-06
vg0706671410 sf0706670415 7 6671410 2.08E-08 6.46E-08
vg0816750102 sf0816747388 8 16750102 7.81E-08 8.28E-06
vg1205463941 sf1205462927 12 5463941 7.84E-08 4.00E-07
vg0407665649 sf0407660916 4 7665649 8.68E-08 5.41E-10
vg0112215171 sf0112214145 1 12215171 1.06E-07 7.56E-07
vg1101412031 sf1101411032 11 1412031 1.41E-07 1.85E-06
vg0706547204 sf0706546209 7 6547204 1.79E-07 1.68E-06
vg1100988118 sf1100987119 11 988118 2.52E-07 2.86E-07
vg0406850673 sf0406846118 4 6850673 2.93E-07 1.03E-06
vg0909042994 sf0909041993 9 9042994 3.52E-07 2.69E-07
vg0405360131 sf0405355572 4 5360131 9.15E-07 NA
vg0324116659 sf0324114738 3 24116659 1.01E-06 1.62E-07
vg0715307926 sf0715306933 7 15307926 1.62E-06 7.67E-07
vg1226826332 sf1226792731 12 26826332 6.69E-06 1.93E-07
vg1210467503 sf1210464916 12 10467503 7.11E-06 3.90E-08
vg1208693304 sf1208690711 12 8693304 NA 1.54E-07
vg0710362097 sf0710361103 7 10362097 NA 3.59E-06