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 mr1980 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
vg1013542980 sf1013471750 10 13542980 1.40E-17 5.63E-13
vg0723699536 sf0723698543 7 23699536 1.07E-10 4.57E-06
vg0723741534 sf0723740541 7 23741534 1.42E-10 3.68E-06
vg0431377813 sf0431192709 4 31377813 5.22E-10 NA
vg0120108656 sf0120107611 1 20108656 7.02E-10 NA
vg1127028421 sf1126556808 11 27028421 7.13E-10 NA
vg0827151098 sf0827148384 8 27151098 7.25E-10 3.71E-06
vg0709674724 sf0709673730 7 9674724 8.55E-09 4.77E-06
vg0232090414 sf0232084545 2 32090414 1.27E-07 NA
vg0629497331 sf0629496333 6 29497331 1.68E-07 1.06E-06
vg1013382554 sf1013311324 10 13382554 2.96E-07 3.88E-06
vg0127820806 sf0127819762 1 27820806 1.06E-06 7.73E-06
vg1012250350 sf1012179165 10 12250350 1.12E-06 1.98E-06
vg1219591736 sf1219563206 12 19591736 1.65E-06 2.48E-06
vg0800647630 sf0800646630 8 647630 3.34E-06 2.99E-06