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 mr1283 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
vg1104990849 sf1104986660 11 4990849 5.85E-09 1.30E-06
vg0820890632 sf0820887919 8 20890632 1.45E-08 1.53E-06
vg0123690615 sf0123689571 1 23690615 1.98E-08 NA
vg0726964336 sf0726963342 7 26964336 7.59E-08 NA
vg0820796944 sf0820794231 8 20796944 9.73E-08 5.80E-07
vg1105269119 sf1105264870 11 5269119 1.14E-07 NA
vg0823213341 sf0823210628 8 23213341 9.28E-07 2.81E-06
vg0819561125 sf0819558412 8 19561125 9.52E-07 1.38E-06