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 mr1312 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
vg0223525077 sf0223519208 2 23525077 8.32E-09 9.13E-08
vg0906112264 sf0906111264 9 6112264 7.77E-08 4.99E-07
vg1209946610 sf1209944020 12 9946610 9.73E-08 6.18E-07
vg0808428148 sf0808427152 8 8428148 2.54E-07 7.19E-07
vg0500906389 sf0500906372 5 906389 2.88E-07 9.46E-07
vg0805992743 sf0805991746 8 5992743 2.97E-07 4.48E-07
vg1105850609 sf1105846361 11 5850609 3.98E-07 1.05E-06
vg0904146189 sf0904145189 9 4146189 5.85E-07 4.61E-07
vg0630442915 sf0630441917 6 30442915 7.06E-07 4.72E-06
vg0630374083 sf0630373085 6 30374083 7.98E-07 2.40E-06
vg0630442371 sf0630441373 6 30442371 8.41E-07 4.69E-06
vg1020531763 sf1020460242 10 20531763 8.55E-07 3.22E-07
vg1218661069 sf1218632504 12 18661069 2.39E-06 4.07E-06
vg0140321570 sf0140320527 1 40321570 2.64E-06 1.51E-06
vg0801697883 sf0801696886 8 1697883 4.47E-06 3.61E-06
vg0335297514 sf0335290383 3 35297514 4.93E-06 4.62E-06
vg0718397736 sf0718396743 7 18397736 NA 1.77E-07
vg0123461399 sf0123460355 1 23461399 NA 2.03E-06
vg0906115244 sf0906114244 9 6115244 NA 3.07E-06