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 mr1746 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
vg0800289042 sf0800288042 8 289042 1.32E-64 1.93E-30
vg0800324457 sf0800323457 8 324457 5.45E-44 1.61E-23
vg0800284313 sf0800283313 8 284313 1.20E-36 7.13E-19
vg0800307523 sf0800306523 8 307523 7.50E-36 1.05E-19
vg0800341569 sf0800340569 8 341569 1.90E-30 3.03E-11
vg0800063298 sf0800062298 8 63298 2.91E-29 3.13E-18
vg0813685508 sf0813682794 8 13685508 4.56E-23 NA
vg0800221627 sf0800220627 8 221627 NA 9.15E-20
vg0800122371 sf0800121371 8 122371 NA 6.02E-10
vg0800438764 sf0800437764 8 438764 NA 8.64E-08
vg1219719232 sf1219690702 12 19719232 NA 1.13E-07
vg0417719148 sf0417547188 4 17719148 NA 3.41E-07
vg0800493307 sf0800492307 8 493307 NA 3.86E-07
vg0223585784 sf0223579915 2 23585784 NA 9.05E-07
vg0523735868 sf0523673289 5 23735868 NA 9.28E-07
vg0223598375 sf0223592506 2 23598375 NA 1.29E-06
vg0726455116 sf0726454122 7 26455116 NA 1.70E-06
vg0800104112 sf0800103112 8 104112 NA 2.36E-06
vg0417872342 sf0417700384 4 17872342 NA 4.47E-06
vg0117840935 sf0117839889 1 17840935 NA 4.51E-06
vg0809216172 sf0809215176 8 9216172 NA 4.53E-06