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 mr1332 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
vg0300353676 sf0300352674 3 353676 3.94E-10 NA
vg0524782801 sf0524720216 5 24782801 1.05E-09 NA
vg0112763835 sf0112762809 1 12763835 3.18E-09 NA
vg0817768586 sf0817765873 8 17768586 3.44E-09 5.65E-08
vg0728114135 sf0728113142 7 28114135 5.43E-09 NA
vg0300245476 sf0300244476 3 245476 8.85E-09 NA
vg1000702985 sf1000701961 10 702985 5.59E-08 1.15E-06
vg1208270538 sf1208267943 12 8270538 1.20E-06 2.77E-06
vg0427788963 sf0427603823 4 27788963 4.69E-06 NA