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 mr1558 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
vg0224661319 sf0224655450 2 24661319 1.48E-10 NA
vg0225424171 sf0225418302 2 25424171 5.85E-10 NA
vg0125465568 sf0125464524 1 25465568 1.29E-09 NA
vg0224880460 sf0224874591 2 24880460 1.71E-09 2.27E-06
vg1212272079 sf1212269417 12 12272079 2.07E-09 NA
vg0224091217 sf0224085348 2 24091217 7.12E-09 NA
vg0222367756 sf0222361887 2 22367756 7.98E-08 NA
vg1209327674 sf1209325083 12 9327674 8.19E-08 2.20E-06
vg0407756297 sf0407751564 4 7756297 1.15E-07 4.20E-06
vg0403670419 sf0403666025 4 3670419 2.71E-07 NA
vg1021148698 sf1021077177 10 21148698 9.70E-07 1.64E-07
vg0522563253 sf0522500695 5 22563253 9.54E-06 NA
vg1109529985 sf1109524562 11 9529985 NA 2.64E-07
vg0823213341 sf0823210628 8 23213341 NA 8.84E-07
vg1019392093 sf1019320648 10 19392093 NA 9.01E-07
vg1019396898 sf1019325453 10 19396898 NA 2.33E-06
vg0707497051 sf0707496056 7 7497051 NA 2.80E-06