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 mr1140 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 4.66E-11 5.85E-08
vg0406944785 sf0406940053 4 6944785 7.04E-11 3.65E-09
vg1218763524 sf1218734959 12 18763524 9.94E-11 2.55E-11
vg0618618072 sf0618617075 6 18618072 3.45E-10 9.80E-09
vg0412100387 sf0412091098 4 12100387 1.42E-09 1.95E-07
vg0222729857 sf0222723988 2 22729857 1.83E-09 8.05E-07
vg0407665649 sf0407660916 4 7665649 2.85E-08 1.75E-10
vg0412144728 sf0412135439 4 12144728 3.23E-08 3.29E-07
vg0402523133 sf0402518738 4 2523133 4.63E-08 1.79E-06
vg0406871301 sf0406866746 4 6871301 4.77E-08 6.41E-07
vg0418306299 sf0418134346 4 18306299 1.30E-07 1.92E-07
vg0406526884 sf0406522327 4 6526884 1.34E-07 2.25E-06
vg0406850673 sf0406846118 4 6850673 1.95E-07 1.22E-06
vg0112215171 sf0112214145 1 12215171 3.76E-07 7.37E-07
vg0706671410 sf0706670415 7 6671410 4.15E-07 2.92E-07
vg1226826332 sf1226792731 12 26826332 4.70E-06 5.77E-07
vg1210467503 sf1210464916 12 10467503 NA 8.56E-07
vg0526374490 sf0526311853 5 26374490 NA 1.52E-06
vg0116837927 sf0116836901 1 16837927 NA 1.78E-06
vg0324116659 sf0324114738 3 24116659 NA 1.86E-06
vg1208693304 sf1208690711 12 8693304 NA 2.62E-06