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 mr1080 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 1.15E-15 3.75E-10
vg0222729857 sf0222723988 2 22729857 2.23E-13 1.85E-08
vg0222744532 sf0222738663 2 22744532 1.67E-12 7.51E-08
vg0616169045 sf0616168047 6 16169045 1.28E-11 9.51E-07
vg0224620629 sf0224614760 2 24620629 5.02E-11 2.87E-06
vg1014721016 sf1014649782 10 14721016 3.06E-09 NA
vg0615245465 sf0615244466 6 15245465 3.21E-09 1.44E-06
vg0412144728 sf0412135439 4 12144728 7.47E-09 9.76E-08
vg0406527945 sf0406523388 4 6527945 2.39E-08 NA
vg0406850673 sf0406846118 4 6850673 4.41E-08 2.80E-06
vg0618618072 sf0618617075 6 18618072 1.01E-07 2.74E-07
vg0406592386 sf0406587830 4 6592386 1.05E-07 5.28E-07
vg1218763524 sf1218734959 12 18763524 1.13E-07 3.53E-08
vg0616244147 sf0616243149 6 16244147 2.34E-07 1.04E-06
vg0906802658 sf0906801658 9 6802658 2.36E-07 8.13E-07
vg0407665649 sf0407660916 4 7665649 2.71E-07 1.33E-09
vg1205810295 sf1205809277 12 5810295 3.21E-07 2.97E-06
vg0112215171 sf0112214145 1 12215171 4.84E-07 2.92E-06
vg0418306299 sf0418134346 4 18306299 1.22E-06 1.11E-06
vg0909042994 sf0909041993 9 9042994 5.51E-06 2.00E-06
vg1210467503 sf1210464916 12 10467503 NA 2.26E-08
vg1112908978 sf1112445299 11 12908978 NA 6.47E-07
vg0401023314 sf0401018866 4 1023314 NA 1.95E-06