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 mr1316 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
vg0700037565 sf0700036565 7 37565 1.14E-14 NA
vg0709146977 sf0709145983 7 9146977 1.66E-14 NA
vg1016765535 sf1016694308 10 16765535 3.88E-14 NA
vg0316032210 sf0316030857 3 16032210 1.23E-13 NA
vg0105240226 sf0105239226 1 5240226 4.15E-13 NA
vg0105148196 sf0105147196 1 5148196 5.74E-11 NA
vg1209591941 sf1209589350 12 9591941 NA 1.34E-06
vg0514055751 sf0513998295 5 14055751 NA 1.48E-06
vg0910454613 sf0910453612 9 10454613 NA 1.72E-06
vg0524699716 sf0524637136 5 24699716 NA 3.12E-06
vg0507694035 sf0507693976 5 7694035 NA 3.14E-06