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 mr1075 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
vg0222741535 sf0222735666 2 22741535 1.20E-103 2.55E-42
vg0222719698 sf0222713829 2 22719698 4.43E-102 1.30E-42
vg0626892999 sf0626892002 6 26892999 1.15E-46 NA
vg0705549134 sf0705548135 7 5549134 1.64E-45 NA
vg0226014278 sf0226008409 2 26014278 7.06E-44 NA
vg0917361897 sf0917360896 9 17361897 1.23E-41 NA
vg0222725003 sf0222719134 2 22725003 NA 2.14E-15
vg0224382271 sf0224376402 2 24382271 NA 2.61E-08
vg0226003155 sf0225997286 2 26003155 NA 1.95E-07
vg0223769163 sf0223763294 2 23769163 NA 2.86E-07
vg0235178362 sf0235172493 2 35178362 NA 5.93E-07
vg1017098012 sf1017026784 10 17098012 NA 6.68E-07
vg0228803563 sf0228797694 2 28803563 NA 6.85E-07
vg0222857256 sf0222851387 2 22857256 NA 9.88E-07
vg0224831654 sf0224825785 2 24831654 NA 1.09E-06
vg0225400091 sf0225394222 2 25400091 NA 2.37E-06
vg0222817468 sf0222811599 2 22817468 NA 4.85E-06