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 mr1512 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
vg0315350100 sf0315348747 3 15350100 2.73E-09 NA
vg0700312059 sf0700311059 7 312059 5.55E-09 NA
vg1013275525 sf1013204295 10 13275525 4.54E-08 NA
vg1122514350 sf1122048221 11 22514350 5.56E-08 NA
vg0422542724 sf0422357611 4 22542724 5.64E-08 NA
vg0406861879 sf0406857324 4 6861879 NA 8.79E-07
vg0715817404 sf0715816411 7 15817404 NA 1.84E-06
vg0520272415 sf0520209888 5 20272415 NA 3.19E-06