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 mr1239 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
vg1100061221 sf1100060221 11 61221 9.52E-07 9.52E-07
vg1120307856 sf1119841780 11 20307856 1.11E-06 1.11E-06
vg1117451309 sf1116985164 11 17451309 1.67E-06 1.67E-06
vg1008209441 sf1008138303 10 8209441 2.40E-06 2.40E-06
vg0606550447 sf0606549448 6 6550447 2.47E-06 2.47E-06
vg0122881740 sf0122880696 1 22881740 4.18E-06 4.18E-06
vg1122447657 sf1121981528 11 22447657 4.62E-06 4.63E-06
vg0314128282 sf0314126971 3 14128282 7.38E-06 7.38E-06