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 mr1636 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
vg0205292054 sf0205292052 2 5292054 1.06E-22 2.38E-08
vg0205287313 sf0205287311 2 5287313 1.39E-22 1.80E-08
vg0726964336 sf0726963342 7 26964336 3.22E-18 NA
vg0140804736 sf0140803693 1 40804736 1.50E-15 NA
vg0714181877 sf0714180884 7 14181877 2.99E-15 NA
vg1105668572 sf1105664324 11 5668572 3.81E-15 NA
vg0527924474 sf0527861831 5 27924474 NA 4.48E-07
vg0518984986 sf0518922470 5 18984986 NA 1.42E-06