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 mr1594 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
vg0717045159 sf0717044166 7 17045159 1.37E-66 2.92E-06
vg1014788162 sf1014716928 10 14788162 7.23E-64 1.69E-06
vg0921958067 sf0921957586 9 21958067 7.47E-64 NA
vg0326760318 sf0326753372 3 26760318 1.72E-63 NA
vg0334602600 sf0334595470 3 34602600 9.68E-63 NA
vg0715801545 sf0715800552 7 15801545 1.08E-60 1.28E-06
vg0523266234 sf0523203655 5 23266234 NA 2.85E-07
vg0310703455 sf0310702371 3 10703455 NA 2.58E-06