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 mr1895 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
vg0916215959 sf0916214958 9 16215959 2.73E-11 NA
vg0700858516 sf0700857516 7 858516 4.80E-11 NA
vg1221869113 sf1221835660 12 21869113 6.65E-11 NA
vg0916326182 sf0916325181 9 16326182 1.07E-10 NA
vg0900284647 sf0900283647 9 284647 1.11E-10 NA
vg0912313203 sf0912312202 9 12313203 1.00E-09 3.03E-06
vg0404713011 sf0404708450 4 4713011 7.02E-08 4.89E-06
vg0138589406 sf0138588363 1 38589406 1.14E-07 NA
vg0516657915 sf0516597557 5 16657915 1.68E-07 NA
vg0804507502 sf0804506505 8 4507502 NA 4.43E-06
vg0434065698 sf0433880590 4 34065698 NA 7.38E-06