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 mr1222 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
vg0222745001 sf0222739132 2 22745001 1.39E-28 2.81E-20
vg0222746186 sf0222740317 2 22746186 1.68E-28 2.32E-20
vg0722959446 sf0722958453 7 22959446 9.43E-13 NA
vg0809946687 sf0809945691 8 9946687 2.76E-12 NA
vg0321480693 sf0321479203 3 21480693 1.42E-11 NA
vg0906131677 sf0906130677 9 6131677 3.54E-11 NA
vg0503366137 sf0503366114 5 3366137 1.77E-10 3.68E-06
vg0529272168 sf0529209523 5 29272168 2.42E-10 1.24E-06
vg0222634177 sf0222628308 2 22634177 3.49E-10 1.40E-06
vg0224832604 sf0224826735 2 24832604 1.56E-07 1.99E-06
vg0222567385 sf0222561516 2 22567385 NA 5.30E-08
vg0524973304 sf0524910719 5 24973304 NA 3.33E-07
vg0224822342 sf0224816473 2 24822342 NA 2.60E-06
vg0222729853 sf0222723984 2 22729853 NA 4.22E-06