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 mr1907 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
vg0524494561 sf0524431982 5 24494561 9.94E-147 2.62E-27
vg0524593054 sf0524530474 5 24593054 1.12E-142 1.01E-28
vg1209153210 sf1209150619 12 9153210 5.46E-103 NA
vg0129939389 sf0129938344 1 29939389 7.76E-103 NA
vg0232358240 sf0232352371 2 32358240 1.31E-100 NA
vg0409271202 sf0409266475 4 9271202 1.22E-98 NA
vg1203688153 sf1203687152 12 3688153 9.74E-94 NA
vg0823513976 sf0823511262 8 23513976 4.63E-92 4.44E-06
vg0217768381 sf0217762512 2 17768381 4.94E-92 4.97E-06
vg0524793384 sf0524730799 5 24793384 NA 1.61E-16
vg0141203398 sf0141202355 1 41203398 NA 1.17E-07
vg0217133318 sf0217127448 2 17133318 NA 2.03E-07
vg0230082779 sf0230076910 2 30082779 NA 2.59E-07
vg0141183119 sf0141182076 1 41183119 NA 1.57E-06
vg0524300922 sf0524238341 5 24300922 NA 1.75E-06
vg0404665726 sf0404661165 4 4665726 NA 2.24E-06
vg1209773540 sf1209770950 12 9773540 NA 3.07E-06
vg1100248726 sf1100247728 11 248726 NA 3.44E-06
vg1221714747 sf1221681294 12 21714747 NA 4.96E-06
vg0322679825 sf0322678314 3 22679825 NA 6.02E-06
vg0729518824 sf0729517832 7 29518824 NA 8.11E-06