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 mr1183 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
vg0128555711 sf0128554666 1 28555711 7.33E-30 NA
vg1104828509 sf1104824411 11 4828509 1.03E-29 NA
vg0726944953 sf0726943959 7 26944953 2.48E-29 NA
vg0138427451 sf0138426408 1 38427451 6.18E-29 NA
vg0628570315 sf0628569317 6 28570315 2.33E-28 NA
vg1128944786 sf1128421565 11 28944786 4.05E-21 NA
vg0222573327 sf0222567458 2 22573327 4.67E-20 3.13E-08
vg0222739831 sf0222733962 2 22739831 NA 8.61E-23
vg1006265706 sf1006281329 10 6265706 NA 4.72E-08
vg0224382271 sf0224376402 2 24382271 NA 1.11E-07
vg1009170287 sf1009099108 10 9170287 NA 1.84E-07
vg1100202473 sf1100201475 11 202473 NA 1.46E-06
vg0224221184 sf0224215315 2 24221184 NA 2.39E-06
vg0223687320 sf0223681451 2 23687320 NA 2.87E-06
vg0223688129 sf0223682260 2 23688129 NA 3.27E-06
vg0728664025 sf0728663033 7 28664025 NA 4.11E-06
vg0222729853 sf0222723984 2 22729853 NA 4.21E-06
vg0223668140 sf0223662271 2 23668140 NA 4.22E-06
vg0224875472 sf0224869603 2 24875472 NA 4.74E-06
vg0718582884 sf0718581891 7 18582884 NA 5.89E-06