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 mr1295 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
vg0908619472 sf0908618471 9 8619472 4.47E-10 NA
vg0314860446 sf0314859093 3 14860446 9.98E-10 NA
vg0204732555 sf0204732552 2 4732555 1.39E-09 NA
vg1126585877 sf1126114292 11 26585877 3.11E-09 9.38E-06
vg0910210790 sf0910209789 9 10210790 3.51E-09 NA
vg1216986135 sf1216980089 12 16986135 6.72E-09 9.80E-08
vg1126346197 sf1125874610 11 26346197 9.53E-09 1.29E-06
vg1127678631 sf1127207018 11 27678631 2.21E-07 5.45E-06
vg1020206725 sf1020135207 10 20206725 3.64E-06 NA
vg0519879638 sf0519817114 5 19879638 4.81E-06 NA
vg1105998802 sf1105994554 11 5998802 6.48E-06 4.83E-06
vg0627018309 sf0627017312 6 27018309 NA 3.67E-07
vg0921125028 sf0921124547 9 21125028 NA 2.15E-06