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 mr1426 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
vg0400043671 sf0400042671 4 43671 2.96E-33 NA
vg0428552941 sf0428367793 4 28552941 2.98E-33 NA
vg0611463000 sf0611462001 6 11463000 7.47E-33 NA
vg0305026907 sf0305025909 3 5026907 3.67E-32 NA
vg0705626790 sf0705625791 7 5626790 3.94E-32 NA
vg0715849539 sf0715848546 7 15849539 3.29E-28 1.22E-06
vg0724513486 sf0724512492 7 24513486 NA 1.75E-07
vg0420830218 sf0420658261 4 20830218 NA 1.17E-06
vg1218168020 sf1218139456 12 18168020 NA 5.15E-06