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 mr1096 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
vg0610566084 sf0610565085 6 10566084 3.92E-133 5.51E-46
vg0610566343 sf0610565344 6 10566343 1.19E-132 2.87E-46
vg0610661117 sf0610660118 6 10661117 6.71E-104 5.89E-32
vg0423897544 sf0423712402 4 23897544 4.23E-69 NA
vg0304965334 sf0304964336 3 4965334 6.73E-69 NA
vg0233932146 sf0233926277 2 33932146 7.07E-69 NA
vg0615150907 sf0615149908 6 15150907 1.14E-68 1.08E-06
vg0617614534 sf0617613537 6 17614534 3.12E-61 2.49E-07
vg0610532672 sf0610531673 6 10532672 NA 6.05E-20
vg0610763769 sf0610762770 6 10763769 NA 1.38E-17
vg0610679715 sf0610678716 6 10679715 NA 5.13E-16
vg0610443193 sf0610442194 6 10443193 NA 4.70E-13
vg0610685711 sf0610684712 6 10685711 NA 6.04E-11
vg0611127784 sf0611126785 6 11127784 NA 2.19E-10
vg0610134394 sf0610133395 6 10134394 NA 7.47E-10
vg0609929059 sf0609928060 6 9929059 NA 4.41E-09
vg0609452459 sf0609451460 6 9452459 NA 5.93E-08
vg0222725824 sf0222719955 2 22725824 NA 9.75E-08
vg0222739831 sf0222733962 2 22739831 NA 1.02E-07
vg0613071268 sf0613070269 6 13071268 NA 1.13E-07
vg0612257699 sf0612256700 6 12257699 NA 5.18E-07
vg0611682950 sf0611681951 6 11682950 NA 6.03E-07
vg0610495424 sf0610494425 6 10495424 NA 6.90E-07
vg0613546054 sf0613545055 6 13546054 NA 7.09E-07
vg0139800351 sf0139799308 1 39800351 NA 1.22E-06
vg0610151699 sf0610150700 6 10151699 NA 1.22E-06
vg0612236193 sf0612235194 6 12236193 NA 2.21E-06
vg0617639143 sf0617638146 6 17639143 NA 2.84E-06
vg0615907055 sf0615906057 6 15907055 NA 2.90E-06