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 mr1225 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
vg0719001778 sf0719000785 7 19001778 1.90E-17 3.49E-12
vg0719007567 sf0719006574 7 19007567 2.07E-17 2.00E-12
vg0719011406 sf0719010413 7 19011406 1.10E-16 7.80E-13
vg0222833455 sf0222827586 2 22833455 3.33E-16 6.96E-14
vg0719449907 sf0719448914 7 19449907 1.81E-13 4.37E-10
vg0719450757 sf0719449764 7 19450757 2.05E-12 1.91E-10
vg0719250400 sf0719249407 7 19250400 9.52E-12 3.17E-08
vg0719076253 sf0719075260 7 19076253 2.63E-10 1.11E-06
vg0719351034 sf0719350041 7 19351034 1.52E-09 4.41E-07
vg0222022581 sf0222016712 2 22022581 1.11E-08 4.34E-06
vg0718885795 sf0718884802 7 18885795 5.81E-08 1.65E-06
vg0719206073 sf0719205080 7 19206073 5.85E-08 8.67E-07
vg0222799084 sf0222793215 2 22799084 1.37E-07 3.24E-06
vg0613011415 sf0613010416 6 13011415 1.02E-06 6.67E-06
vg0228211407 sf0228205538 2 28211407 2.55E-06 1.40E-06
vg0222861576 sf0222855707 2 22861576 5.77E-06 1.37E-06
vg0222523726 sf0222517857 2 22523726 NA 4.16E-06