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 mr1905 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
vg0805970880 sf0805969883 8 5970880 6.60E-15 1.10E-07
vg0805944930 sf0805943933 8 5944930 7.00E-15 3.70E-08
vg0314797580 sf0314796267 3 14797580 3.89E-14 1.79E-06
vg1115925850 sf1115460720 11 15925850 1.03E-13 8.59E-07
vg0228537663 sf0228531794 2 28537663 1.49E-13 6.95E-07
vg0332611601 sf0332604472 3 32611601 2.33E-13 NA
vg0812629955 sf0812627780 8 12629955 6.65E-13 4.11E-06
vg0409858762 sf0409849460 4 9858762 7.58E-13 3.72E-06
vg0332522340 sf0332515213 3 32522340 9.97E-13 NA
vg0308008402 sf0308007340 3 8008402 1.04E-12 4.77E-06
vg0921539163 sf0921538682 9 21539163 1.82E-09 2.59E-07
vg0228184061 sf0228178192 2 28184061 1.84E-09 3.29E-08
vg1214656787 sf1214654127 12 14656787 NA 5.33E-07
vg1125281578 sf1124815418 11 25281578 NA 7.85E-07
vg0805968808 sf0805967811 8 5968808 NA 1.01E-06
vg0310368348 sf0310367264 3 10368348 NA 1.49E-06
vg1215090726 sf1215088067 12 15090726 NA 1.76E-06
vg1201256540 sf1201255540 12 1256540 NA 2.20E-06
vg0818200735 sf0818198022 8 18200735 NA 4.52E-06