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 mr1248 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
vg0216893269 sf0216887399 2 16893269 6.04E-17 3.62E-09
vg0216876466 sf0216870596 2 16876466 6.93E-17 2.45E-09
vg1002771978 sf1002770955 10 2771978 1.89E-12 3.71E-07
vg0720001553 sf0720000560 7 20001553 1.42E-11 NA
vg1017647167 sf1017575940 10 17647167 4.93E-11 NA
vg0800332417 sf0800331417 8 332417 7.89E-11 NA
vg0712648528 sf0712647535 7 12648528 3.15E-09 NA
vg0420788121 sf0420616164 4 20788121 2.86E-08 2.89E-06
vg1216434924 sf1216432217 12 16434924 7.77E-07 1.77E-07
vg0819862457 sf0819859744 8 19862457 NA 1.43E-07
vg0334445299 sf0334438169 3 34445299 NA 4.25E-07
vg0803630862 sf0803629865 8 3630862 NA 5.00E-07
vg0423871567 sf0423686425 4 23871567 NA 7.29E-07
vg0631201159 sf0631200161 6 31201159 NA 1.83E-06
vg0520857344 sf0520794785 5 20857344 NA 1.87E-06
vg0500335511 sf0500335511 5 335511 NA 2.60E-06
vg0907533269 sf0907532269 9 7533269 NA 3.52E-06
vg0323995709 sf0323993883 3 23995709 NA 4.36E-06
vg1002824453 sf1002823430 10 2824453 NA 4.56E-06