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 mr1185 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
vg1105906564 sf1105902316 11 5906564 2.69E-09 2.56E-06
vg1105925054 sf1105920806 11 5925054 3.24E-09 9.55E-06
vg1105907265 sf1105903017 11 5907265 3.68E-09 2.33E-06
vg1217046290 sf1217040244 12 17046290 2.00E-08 NA
vg0919811754 sf0919811273 9 19811754 2.86E-08 NA
vg0133176503 sf0133175459 1 33176503 3.15E-08 NA
vg1105448751 sf1105444502 11 5448751 9.99E-08 NA
vg0922613922 sf0922613441 9 22613922 1.82E-07 5.81E-07
vg0310177475 sf0310176391 3 10177475 1.20E-06 8.69E-07
vg0522974317 sf0522911758 5 22974317 1.95E-06 4.56E-06
vg0412475075 sf0412465790 4 12475075 3.33E-06 8.27E-06
vg0413435949 sf0413426663 4 13435949 4.55E-06 2.31E-06
vg0420830218 sf0420658261 4 20830218 NA 7.79E-07
vg0506745303 sf0506745245 5 6745303 NA 3.87E-06