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 mr1146 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
vg0222743526 sf0222737657 2 22743526 5.90E-51 1.01E-28
vg0222746050 sf0222740181 2 22746050 1.03E-50 3.77E-29
vg1207773391 sf1207770797 12 7773391 2.50E-21 NA
vg0722483807 sf0722482814 7 22483807 3.18E-21 NA
vg0406998246 sf0406993517 4 6998246 1.03E-20 NA
vg0713719162 sf0713718169 7 13719162 2.07E-20 NA
vg1215239496 sf1215236793 12 15239496 9.74E-19 3.36E-06
vg0220963033 sf0220957165 2 20963033 2.43E-17 NA
vg0125220764 sf0125219720 1 25220764 4.80E-17 NA
vg0222725003 sf0222719134 2 22725003 NA 2.62E-17
vg0222817468 sf0222811599 2 22817468 NA 4.85E-07
vg0524971409 sf0524908824 5 24971409 NA 9.92E-07
vg0224676560 sf0224670691 2 24676560 NA 1.10E-06
vg0222558409 sf0222552540 2 22558409 NA 1.47E-06
vg0525072434 sf0525009849 5 25072434 NA 1.89E-06
vg0433003871 sf0432818757 4 33003871 NA 3.88E-06
vg0222735022 sf0222729153 2 22735022 NA 4.39E-06
vg0211185461 sf0211185458 2 11185461 NA 6.14E-06