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 mr1378 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
vg0123684702 sf0123683658 1 23684702 3.55E-16 NA
vg0141705283 sf0141704240 1 41705283 8.39E-15 NA
vg0131627835 sf0131626791 1 31627835 1.80E-14 NA
vg0138428840 sf0138427797 1 38428840 1.91E-14 NA
vg0128383640 sf0128382596 1 28383640 3.26E-14 NA
vg0726962702 sf0726961708 7 26962702 1.85E-11 3.88E-06
vg0918422796 sf0918421795 9 18422796 2.49E-10 NA
vg0507386923 sf0507386865 5 7386923 4.22E-08 NA
vg0713247684 sf0713246691 7 13247684 NA 1.35E-06
vg0717367275 sf0717366282 7 17367275 NA 2.14E-06
vg0224587441 sf0224581572 2 24587441 NA 4.64E-06