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 mr1730 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
vg0726714837 sf0726713843 7 26714837 2.57E-23 1.44E-06
vg0726726990 sf0726725996 7 26726990 6.21E-23 1.16E-06
vg1215239496 sf1215236793 12 15239496 4.64E-22 NA
vg0825340856 sf0825338142 8 25340856 1.39E-21 NA
vg0307075857 sf0307074855 3 7075857 2.36E-20 NA
vg0127892829 sf0127891785 1 27892829 5.68E-20 NA
vg0413759612 sf0413750326 4 13759612 NA 1.24E-14
vg0413764976 sf0413755690 4 13764976 NA 1.75E-14
vg0414050911 sf0414041626 4 14050911 NA 3.23E-10
vg0414059272 sf0414049987 4 14059272 NA 3.52E-08
vg0322159734 sf0322158241 3 22159734 NA 6.55E-07
vg1215652345 sf1215649642 12 15652345 NA 1.37E-06
vg0317322249 sf0317321059 3 17322249 NA 2.16E-06
vg0100994949 sf0100956946 1 994949 NA 2.37E-06
vg1219590404 sf1219561874 12 19590404 NA 2.64E-06
vg1219593045 sf1219564515 12 19593045 NA 4.17E-06
vg0404016759 sf0404012366 4 4016759 NA 4.64E-06