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 mr1526 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
vg0610608211 sf0610607212 6 10608211 5.39E-107 7.81E-32
vg0610608095 sf0610607096 6 10608095 3.44E-106 2.30E-34
vg0709180653 sf0709179659 7 9180653 9.08E-66 NA
vg0617621981 sf0617620984 6 17621981 1.67E-64 NA
vg0705560234 sf0705559235 7 5560234 2.44E-64 NA
vg0715964913 sf0715963920 7 15964913 8.59E-64 NA
vg0610678495 sf0610677496 6 10678495 5.39E-62 8.46E-18
vg0234922136 sf0234916267 2 34922136 3.11E-61 2.07E-07
vg0303148156 sf0303147152 3 3148156 3.02E-57 1.77E-07
vg0610679715 sf0610678716 6 10679715 NA 8.41E-12
vg0610134394 sf0610133395 6 10134394 NA 8.47E-12
vg0610763769 sf0610762770 6 10763769 NA 7.01E-11
vg0610443193 sf0610442194 6 10443193 NA 2.85E-09
vg0610674214 sf0610673215 6 10674214 NA 8.79E-09
vg0611127784 sf0611126785 6 11127784 NA 5.22E-08
vg0609929059 sf0609928060 6 9929059 NA 6.01E-07
vg0206663515 sf0206663515 2 6663515 NA 6.40E-07
vg0608451968 sf0608450969 6 8451968 NA 9.44E-07
vg0609902440 sf0609901441 6 9902440 NA 1.26E-06
vg1218089575 sf1218061011 12 18089575 NA 1.92E-06
vg0614110509 sf0614109510 6 14110509 NA 1.96E-06
vg0332720125 sf0332712996 3 32720125 NA 2.07E-06
vg0613809145 sf0613808146 6 13809145 NA 2.29E-06
vg0610936973 sf0610935974 6 10936973 NA 2.86E-06
vg0610548167 sf0610547168 6 10548167 NA 3.35E-06
vg1103833072 sf1103828974 11 3833072 NA 7.69E-06