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 mr1254 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
vg0222743526 sf0222737657 2 22743526 8.71E-22 7.62E-17
vg0222743508 sf0222737639 2 22743508 1.38E-21 5.55E-17
vg0300244272 sf0300243272 3 244272 1.33E-10 4.82E-07
vg0323778716 sf0323776890 3 23778716 3.15E-09 NA
vg0222765370 sf0222759501 2 22765370 5.67E-09 1.58E-06
vg0224875540 sf0224869671 2 24875540 5.74E-09 NA
vg0222799385 sf0222793516 2 22799385 1.96E-08 9.09E-07
vg0424051023 sf0423865884 4 24051023 5.53E-07 NA
vg0224129317 sf0224123448 2 24129317 7.01E-07 7.67E-07
vg1109865477 sf1109860054 11 9865477 NA 3.73E-06