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 mr1022 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
vg1215966676 sf1215963972 12 15966676 3.02E-89 1.46E-35
vg1215969713 sf1215967009 12 15969713 1.11E-69 2.54E-28
vg1210337904 sf1210335317 12 10337904 4.49E-50 1.51E-06
vg1209186897 sf1209184306 12 9186897 4.44E-45 1.83E-09
vg1212938220 sf1212935559 12 12938220 1.15E-41 6.89E-08
vg1223855525 sf1223821978 12 23855525 1.43E-38 1.31E-07
vg1223855613 sf1223822066 12 23855613 1.68E-38 3.75E-08
vg1219911712 sf1219883182 12 19911712 2.43E-37 NA
vg1215359795 sf1215357093 12 15359795 3.88E-34 3.79E-09
vg1215857575 sf1215854871 12 15857575 7.59E-30 3.11E-17
vg1215871822 sf1215869118 12 15871822 NA 3.40E-09
vg1216993151 sf1216987105 12 16993151 NA 3.55E-09
vg1215978234 sf1215975530 12 15978234 NA 4.49E-09
vg0610620315 sf0610619316 6 10620315 NA 2.48E-08
vg1215809668 sf1215806965 12 15809668 NA 4.69E-08
vg0318244684 sf0318243466 3 18244684 NA 5.11E-07
vg0218141493 sf0218135624 2 18141493 NA 1.83E-06
vg0224688934 sf0224683065 2 24688934 NA 2.13E-06
vg0429681265 sf0429496133 4 29681265 NA 4.43E-06