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 mr1499 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
vg0234255542 sf0234249673 2 34255542 6.62E-08 NA
vg0232481318 sf0232475449 2 32481318 3.11E-07 4.58E-07
vg0606569149 sf0606568150 6 6569149 1.32E-06 8.92E-07
vg1113148610 sf1112684931 11 13148610 1.73E-06 NA
vg0307302619 sf0307301617 3 7302619 NA 2.59E-07
vg0229412816 sf0229406947 2 29412816 NA 7.86E-07
vg0810807387 sf0810806392 8 10807387 NA 1.13E-06
vg0801569471 sf0801568473 8 1569471 NA 1.56E-06
vg0122500370 sf0122499325 1 22500370 NA 2.91E-06
vg0400690241 sf0400689240 4 690241 NA 3.41E-06
vg0813259068 sf0813256623 8 13259068 NA 3.89E-06