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 mr1595 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
vg1110480312 sf1110474857 11 10480312 6.03E-15 8.19E-06
vg0222725881 sf0222720012 2 22725881 6.39E-13 7.26E-07
vg1116407848 sf1115942725 11 16407848 3.12E-12 NA
vg0720924027 sf0720923034 7 20924027 9.46E-12 NA
vg0324615779 sf0324613858 3 24615779 1.08E-11 NA
vg0719449286 sf0719448293 7 19449286 7.15E-11 1.95E-07
vg0221017884 sf0221012016 2 21017884 3.49E-10 NA
vg1110487259 sf1110481804 11 10487259 7.88E-10 NA
vg0717319936 sf0717318943 7 17319936 9.93E-09 NA
vg0215381884 sf0215376014 2 15381884 NA 1.09E-06