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 mr1618 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
vg0406995300 sf0406990571 4 6995300 1.08E-11 6.47E-09
vg0406944785 sf0406940053 4 6944785 1.99E-11 4.45E-09
vg0616169045 sf0616168047 6 16169045 3.52E-10 1.78E-06
vg1226691665 sf1226658061 12 26691665 7.01E-10 1.80E-06
vg0618618072 sf0618617075 6 18618072 1.23E-09 2.95E-08
vg0615245465 sf0615244466 6 15245465 1.33E-09 1.86E-07
vg1218763524 sf1218734959 12 18763524 1.64E-09 1.51E-09
vg0412100387 sf0412091098 4 12100387 1.68E-09 4.42E-07
vg0402523133 sf0402518738 4 2523133 4.78E-09 2.00E-06
vg1205463941 sf1205462927 12 5463941 1.86E-08 3.75E-07
vg0112215171 sf0112214145 1 12215171 8.61E-08 8.52E-07
vg0406862446 sf0406857891 4 6862446 1.16E-07 9.61E-07
vg0706671410 sf0706670415 7 6671410 1.78E-07 8.16E-08
vg0407665649 sf0407660916 4 7665649 2.00E-07 1.04E-09
vg0122564570 sf0122563525 1 22564570 8.28E-07 NA
vg0418306299 sf0418134346 4 18306299 1.07E-06 1.18E-06
vg0222729797 sf0222723928 2 22729797 1.29E-06 NA
vg0715307926 sf0715306933 7 15307926 4.17E-06 1.01E-06
vg0324116659 sf0324114738 3 24116659 4.71E-06 1.01E-06
vg1226826332 sf1226792731 12 26826332 5.89E-06 2.84E-07
vg1208693304 sf1208690711 12 8693304 9.35E-06 1.46E-06
vg0709331066 sf0709330072 7 9331066 NA 9.63E-07
vg1210467503 sf1210464916 12 10467503 NA 1.01E-06