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 mr1277 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
vg0433932504 sf0433747400 4 33932504 8.43E-10 9.35E-06
vg0420329083 sf0420157127 4 20329083 1.10E-09 NA
vg0904833940 sf0904832940 9 4833940 4.11E-09 NA
vg0713218164 sf0713217171 7 13218164 4.32E-09 NA
vg0710453528 sf0710452534 7 10453528 4.53E-09 NA
vg0818053416 sf0818050703 8 18053416 8.47E-08 NA
vg0402509050 sf0402504653 4 2509050 6.00E-07 NA
vg0410881366 sf0410872067 4 10881366 7.76E-07 NA