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 mr1718 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
vg0321134351 sf0321132861 3 21134351 1.94E-150 7.63E-22
vg0321285180 sf0321283690 3 21285180 2.11E-150 1.59E-24
vg0317721273 sf0317720055 3 17721273 1.63E-141 8.95E-18
vg0323653572 sf0323651746 3 23653572 1.12E-126 NA
vg0522255261 sf0522192702 5 22255261 3.75E-121 NA
vg0501560528 sf0501560512 5 1560528 2.88E-120 NA
vg0522082238 sf0522019680 5 22082238 7.03E-117 3.96E-06
vg0501575258 sf0501575242 5 1575258 6.75E-113 2.83E-06
vg0100183346 sf0100182346 1 183346 NA 2.02E-08
vg0208223979 sf0208223978 2 8223979 NA 1.13E-06
vg0100296979 sf0100295979 1 296979 NA 2.46E-06
vg1121620131 sf1121154008 11 21620131 NA 2.87E-06
vg0523491706 sf0523429127 5 23491706 NA 3.08E-06
vg0523549315 sf0523486736 5 23549315 NA 3.19E-06
vg1121410763 sf1120944640 11 21410763 NA 4.67E-06
vg0504907926 sf0504907904 5 4907926 NA 4.69E-06
vg0719131210 sf0719130217 7 19131210 NA 4.75E-06
vg1216569286 sf1216566579 12 16569286 NA 6.24E-06
vg1121618472 sf1121152349 11 21618472 NA 7.74E-06