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 mr1035 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
vg0405531572 sf0405527013 4 5531572 2.79E-13 9.33E-11
vg0405488386 sf0405483827 4 5488386 6.43E-13 5.01E-11
vg0405256292 sf0405251733 4 5256292 9.02E-11 3.73E-06
vg0405249660 sf0405245101 4 5249660 1.03E-10 2.97E-06
vg0405694545 sf0405689984 4 5694545 8.37E-09 1.19E-06
vg0424992689 sf0424807550 4 24992689 2.41E-08 NA
vg0405302070 sf0405297511 4 5302070 2.58E-08 1.43E-06
vg0406863298 sf0406858743 4 6863298 1.14E-07 2.31E-06
vg0405993315 sf0405988755 4 5993315 2.58E-07 2.47E-06
vg0404256297 sf0404251903 4 4256297 3.09E-07 1.04E-06
vg0615097742 sf0615096743 6 15097742 3.13E-07 2.64E-06
vg0406861364 sf0406856809 4 6861364 3.82E-07 1.85E-06
vg1215431363 sf1215428661 12 15431363 6.98E-07 1.52E-06
vg1118328578 sf1117862436 11 18328578 3.23E-06 NA
vg0404027324 sf0404022931 4 4027324 6.39E-06 2.26E-07
vg1205810555 sf1205809537 12 5810555 NA 1.93E-06