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 mr1137 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
vg0604350087 sf0604349088 6 4350087 1.10E-73 2.11E-37
vg0604357002 sf0604356003 6 4357002 1.19E-73 2.05E-37
vg0207150816 sf0207150816 2 7150816 7.23E-45 4.19E-13
vg1021135316 sf1021063795 10 21135316 2.28E-40 6.07E-07
vg1224843226 sf1224809680 12 24843226 3.66E-40 7.22E-07
vg0313641931 sf0313640648 3 13641931 1.10E-37 7.77E-09
vg0910028393 sf0910027392 9 10028393 2.85E-37 4.45E-09
vg0912901940 sf0912900939 9 12901940 4.38E-37 2.65E-07
vg0128528170 sf0128527125 1 28528170 1.95E-35 8.00E-09
vg1000904661 sf1000903637 10 904661 3.78E-34 6.78E-08
vg0808821102 sf0808820106 8 8821102 6.79E-34 2.31E-07
vg0702730576 sf0702729577 7 2730576 8.56E-34 3.52E-08
vg1223038204 sf1223004664 12 23038204 5.75E-32 3.05E-09
vg0216502492 sf0216496622 2 16502492 1.10E-31 2.82E-07
vg1123325178 sf1122859048 11 23325178 1.11E-31 2.89E-08
vg0617571208 sf0617570211 6 17571208 1.09E-30 4.86E-08
vg0401281473 sf0401277023 4 1281473 1.66E-30 2.51E-09
vg1116506738 sf1116041615 11 16506738 2.40E-30 4.24E-09
vg0604237628 sf0604236629 6 4237628 NA 6.81E-15
vg0604373917 sf0604372918 6 4373917 NA 2.17E-13
vg0604439758 sf0604438759 6 4439758 NA 5.65E-13
vg0604317901 sf0604316902 6 4317901 NA 4.12E-11
vg0701270194 sf0701269194 7 1270194 NA 4.40E-09
vg0601465470 sf0601464471 6 1465470 NA 1.33E-08
vg0604303918 sf0604302919 6 4303918 NA 1.73E-08
vg1114197693 sf1113734014 11 14197693 NA 1.09E-07
vg0601481283 sf0601480284 6 1481283 NA 1.17E-07
vg0803502519 sf0803501522 8 3502519 NA 1.41E-07