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 mr1598 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
vg0918924718 sf0918923718 9 18924718 6.54E-68 1.24E-18
vg0908878156 sf0908877155 9 8878156 1.15E-44 NA
vg1221931538 sf1221898085 12 21931538 1.53E-44 NA
vg0912199448 sf0912198447 9 12199448 5.26E-44 NA
vg0722668231 sf0722667238 7 22668231 4.14E-42 NA
vg0918487266 sf0918486265 9 18487266 7.51E-42 1.18E-10
vg0912275276 sf0912274275 9 12275276 3.44E-35 5.19E-07
vg0918496669 sf0918495668 9 18496669 NA 7.70E-14
vg0123073078 sf0123072034 1 23073078 NA 2.83E-08
vg0919230563 sf0919230153 9 19230563 NA 5.78E-08
vg0917357322 sf0917356321 9 17357322 NA 1.91E-07
vg0914888205 sf0914887204 9 14888205 NA 2.27E-06
vg1011249793 sf1011178613 10 11249793 NA 3.66E-06