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 mr1477 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
vg0127650549 sf0127649505 1 27650549 1.11E-23 NA
vg0232621709 sf0232615840 2 32621709 1.20E-23 NA
vg0728914146 sf0728913154 7 28914146 1.41E-23 NA
vg0611856752 sf0611855753 6 11856752 1.45E-23 NA
vg1020742613 sf1020671092 10 20742613 1.77E-23 9.07E-06
vg1004624542 sf1004641080 10 4624542 NA 3.38E-08
vg1222419954 sf1222386393 12 22419954 NA 1.77E-06
vg1004618983 sf1004635521 10 4618983 NA 2.77E-06
vg0138093125 sf0138092082 1 38093125 NA 3.72E-06
vg0138341455 sf0138340412 1 38341455 NA 5.89E-06
vg0608916603 sf0608915604 6 8916603 NA 8.53E-06
vg0721287216 sf0721286223 7 21287216 NA 8.67E-06