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 mr1750 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
vg0321220629 sf0321219139 3 21220629 3.24E-263 4.62E-47
vg0321369281 sf0321367791 3 21369281 2.00E-261 4.74E-47
vg0321280504 sf0321279014 3 21280504 3.63E-247 9.99E-41
vg0321273503 sf0321272013 3 21273503 1.47E-238 2.23E-34
vg0317721273 sf0317720055 3 17721273 7.74E-234 4.84E-28
vg0317754398 sf0317753180 3 17754398 8.42E-234 4.29E-29
vg0323864753 sf0323862927 3 23864753 5.99E-183 1.65E-07
vg0324349110 sf0324347189 3 24349110 5.13E-179 6.11E-13
vg0330461904 sf0330454793 3 30461904 2.01E-176 NA
vg0327763388 sf0327756441 3 27763388 3.77E-175 4.84E-08
vg0327747214 sf0327740267 3 27747214 2.82E-164 1.92E-09
vg0230101399 sf0230095530 2 30101399 3.28E-151 1.57E-07
vg0130044397 sf0130043352 1 30044397 NA 1.50E-08
vg0825891876 sf0825889162 8 25891876 NA 2.25E-07
vg0101266799 sf0101265799 1 1266799 NA 2.32E-07
vg1226229451 sf1226195845 12 26229451 NA 2.67E-07
vg0615849876 sf0615848878 6 15849876 NA 4.04E-07
vg0320914714 sf0320913224 3 20914714 NA 4.74E-07
vg0604095633 sf0604094634 6 4095633 NA 4.83E-07
vg1217048528 sf1217042482 12 17048528 NA 5.15E-07
vg0321114139 sf0321112649 3 21114139 NA 5.35E-07
vg1208915362 sf1208912770 12 8915362 NA 6.00E-07
vg0522802477 sf0522739919 5 22802477 NA 6.25E-07
vg0501608561 sf0501608545 5 1608561 NA 7.67E-07
vg0320632634 sf0320631144 3 20632634 NA 7.69E-07
vg0140900473 sf0140899430 1 40900473 NA 9.16E-07
vg0527445807 sf0527383163 5 27445807 NA 9.23E-07
vg0302293724 sf0302292720 3 2293724 NA 1.22E-06