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 mr1884 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
vg1216247174 sf1216244470 12 16247174 8.31E-09 3.20E-07
vg1218105268 sf1218076704 12 18105268 1.78E-07 3.70E-06
vg1208153687 sf1208151093 12 8153687 1.84E-07 3.02E-06
vg0100043649 sf0100042649 1 43649 5.46E-07 3.45E-06
vg0207688311 sf0207688311 2 7688311 5.97E-07 4.89E-06