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 mr1621 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
vg0139829401 sf0139828358 1 39829401 2.75E-12 9.10E-06
vg1218522379 sf1218493815 12 18522379 1.96E-10 NA
vg0139606443 sf0139605400 1 39606443 4.39E-10 2.76E-06
vg0703117572 sf0703116573 7 3117572 5.64E-10 NA
vg0139594503 sf0139593460 1 39594503 6.27E-10 2.52E-06
vg0623452196 sf0623451199 6 23452196 2.44E-09 NA
vg1218162333 sf1218133769 12 18162333 2.60E-08 7.65E-07
vg1218112515 sf1218083951 12 18112515 4.15E-07 4.63E-09
vg0815721034 sf0815718320 8 15721034 2.85E-06 1.14E-06
vg0224382766 sf0224376897 2 24382766 4.12E-06 3.53E-06
vg1218153582 sf1218125018 12 18153582 NA 4.13E-08
vg1218154986 sf1218126422 12 18154986 NA 1.31E-06
vg0118783367 sf0118782322 1 18783367 NA 4.55E-06