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 mr1642 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
vg0125680354 sf0125679310 1 25680354 1.22E-16 NA
vg0724465961 sf0724464967 7 24465961 5.52E-16 NA
vg0422013922 sf0421841973 4 22013922 1.49E-15 NA
vg0903180038 sf0903179038 9 3180038 4.14E-15 NA
vg0434392194 sf0434207088 4 34392194 7.49E-15 NA
vg0920196604 sf0920196123 9 20196604 5.68E-12 1.53E-07
vg0908755951 sf0908754950 9 8755951 4.48E-11 1.30E-06
vg0903356460 sf0903355460 9 3356460 5.83E-11 4.19E-06
vg1117950562 sf1117484420 11 17950562 3.70E-10 2.02E-06
vg0903264298 sf0903263298 9 3264298 9.08E-08 NA
vg0804879390 sf0804878393 8 4879390 NA 9.10E-07
vg0123838334 sf0123837290 1 23838334 NA 2.47E-06
vg1215355318 sf1215352616 12 15355318 NA 3.09E-06