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 mr1653 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
vg0719065475 sf0719064482 7 19065475 2.38E-31 NA
vg1105668680 sf1105664432 11 5668680 4.68E-31 NA
vg0138424728 sf0138423685 1 38424728 6.67E-31 NA
vg0113515835 sf0113514809 1 13515835 1.21E-30 NA
vg0307487923 sf0307486861 3 7487923 2.53E-30 NA
vg0815517828 sf0815515114 8 15517828 8.24E-28 3.68E-06
vg1102149285 sf1102145143 11 2149285 6.49E-26 NA
vg0706162756 sf0706161757 7 6162756 NA 3.37E-07
vg1016428635 sf1016357409 10 16428635 NA 2.36E-06
vg1115522117 sf1115058430 11 15522117 NA 3.36E-06
vg0409858762 sf0409849460 4 9858762 NA 3.77E-06
vg1116689982 sf1116224859 11 16689982 NA 4.11E-06
vg1017269903 sf1017198676 10 17269903 NA 6.71E-06