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 mr1098 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
vg0222747179 sf0222741310 2 22747179 6.84E-36 2.42E-29
vg0222726563 sf0222720694 2 22726563 2.75E-35 1.34E-29
vg0222765370 sf0222759501 2 22765370 5.66E-12 8.69E-09
vg0224875540 sf0224869671 2 24875540 8.79E-12 4.56E-07
vg0224876386 sf0224870517 2 24876386 9.86E-12 2.17E-07
vg0223718136 sf0223712267 2 23718136 3.73E-11 2.10E-07
vg0223738930 sf0223733061 2 23738930 9.51E-11 5.29E-07
vg0222634177 sf0222628308 2 22634177 1.49E-10 1.54E-06
vg0222661859 sf0222655990 2 22661859 3.77E-08 6.76E-09
vg0222799371 sf0222793502 2 22799371 3.29E-07 3.59E-07
vg0114126056 sf0114125030 1 14126056 2.65E-06 NA
vg0222398309 sf0222392440 2 22398309 3.70E-06 1.40E-06
vg0525239875 sf0525177296 5 25239875 NA 1.62E-06
vg0316040822 sf0316039469 3 16040822 NA 2.20E-06
vg0224832469 sf0224826600 2 24832469 NA 2.20E-06