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 mr1589 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
vg0222747179 sf0222741310 2 22747179 2.21E-32 7.53E-28
vg0222726032 sf0222720163 2 22726032 2.31E-32 4.00E-28
vg0222634177 sf0222628308 2 22634177 1.04E-11 2.78E-08
vg0224876386 sf0224870517 2 24876386 1.80E-11 4.96E-08
vg0224872829 sf0224866960 2 24872829 4.47E-11 3.88E-08
vg0223077967 sf0223072098 2 23077967 1.97E-10 1.18E-07
vg0222765370 sf0222759501 2 22765370 2.06E-10 3.69E-07
vg0224623246 sf0224617377 2 24623246 3.59E-10 5.59E-08
vg0223078170 sf0223072301 2 23078170 1.21E-09 4.54E-07
vg0222016029 sf0222010160 2 22016029 4.71E-09 1.10E-06
vg0222799385 sf0222793516 2 22799385 3.52E-08 4.15E-07
vg0224274080 sf0224268211 2 24274080 1.70E-07 2.31E-06
vg0222879623 sf0222873754 2 22879623 2.96E-07 3.18E-07
vg0222615084 sf0222609215 2 22615084 4.64E-07 4.59E-06
vg0727277584 sf0727276590 7 27277584 1.34E-06 2.96E-06
vg0224832469 sf0224826600 2 24832469 NA 9.29E-07
vg0222398309 sf0222392440 2 22398309 NA 1.01E-06