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 mr1662 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
vg1125470232 sf1125004071 11 25470232 1.87E-42 3.14E-26
vg1125443769 sf1124977608 11 25443769 9.13E-19 4.23E-11
vg1125471656 sf1125005495 11 25471656 1.22E-17 1.27E-14
vg1125546169 sf1125080008 11 25546169 1.25E-17 1.59E-09
vg1125385406 sf1124919245 11 25385406 3.55E-16 2.01E-19
vg0432437759 sf0432252650 4 32437759 1.30E-14 3.50E-07
vg1125089739 sf1124623579 11 25089739 6.46E-14 4.75E-08
vg1127814672 sf1127343058 11 27814672 2.31E-13 2.48E-07
vg1125077990 sf1124611830 11 25077990 1.33E-12 3.45E-08
vg1125663697 sf1125197536 11 25663697 2.35E-11 5.29E-07
vg1125474766 sf1125008605 11 25474766 2.62E-11 3.45E-07
vg1125881170 sf1125415089 11 25881170 9.36E-11 7.20E-07
vg1124459457 sf1123993297 11 24459457 3.78E-10 1.34E-06
vg1127691454 sf1127219841 11 27691454 7.09E-10 1.17E-06
vg1125231256 sf1124765096 11 25231256 1.92E-09 8.51E-10
vg1125418465 sf1124952304 11 25418465 1.98E-09 1.27E-11
vg1125171187 sf1124705027 11 25171187 3.63E-09 1.43E-10
vg1219745087 sf1219716557 12 19745087 8.98E-08 4.09E-07
vg1125323327 sf1124857167 11 25323327 4.89E-07 4.71E-07
vg1125239418 sf1124773258 11 25239418 NA 1.00E-07
vg0211188937 sf0211188934 2 11188937 NA 1.97E-07
vg1125256580 sf1124790420 11 25256580 NA 1.24E-06