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 mr1343 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
vg0724515347 sf0724514353 7 24515347 3.02E-16 3.02E-16
vg0400871651 sf0400870651 4 871651 7.39E-12 7.39E-12
vg0400999452 sf0400995004 4 999452 2.55E-09 2.55E-09
vg0422741082 sf0422555965 4 22741082 3.51E-09 3.51E-09
vg0230466138 sf0230460269 2 30466138 5.23E-09 5.23E-09
vg1122003288 sf1121537159 11 22003288 6.94E-08 6.94E-08
vg1117548144 sf1117082000 11 17548144 1.17E-07 1.17E-07
vg0803137680 sf0803136683 8 3137680 1.69E-07 1.69E-07
vg0624044738 sf0624043741 6 24044738 1.76E-07 1.76E-07
vg0724533734 sf0724532740 7 24533734 1.84E-07 1.84E-07
vg0233606717 sf0233600848 2 33606717 2.03E-07 2.04E-07
vg0612544297 sf0612543298 6 12544297 2.99E-07 2.99E-07
vg0418762497 sf0418590542 4 18762497 4.80E-07 4.80E-07
vg0411669826 sf0411660532 4 11669826 4.85E-07 4.85E-07
vg1219795565 sf1219767035 12 19795565 5.53E-07 5.53E-07
vg0215723095 sf0215717225 2 15723095 5.75E-07 5.75E-07
vg1207993699 sf1207991105 12 7993699 7.70E-07 7.70E-07
vg1217880052 sf1217851486 12 17880052 8.10E-07 8.11E-07
vg0824308543 sf0824305829 8 24308543 8.91E-07 8.91E-07
vg0728925896 sf0728924904 7 28925896 9.25E-07 9.25E-07