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
vg0222719604 sf0222713735 2 22719604 3.71E-21 8.76E-11
vg0812498626 sf0812497530 8 12498626 5.48E-15 NA
vg0304001174 sf0304000170 3 4001174 3.60E-13 NA
vg0209194358 sf0209194356 2 9194358 1.12E-12 NA
vg0626896449 sf0626895452 6 26896449 1.21E-12 NA
vg0316269128 sf0316267775 3 16269128 NA 1.62E-06
vg0427400029 sf0427214893 4 27400029 NA 2.78E-06
vg0326004558 sf0326002578 3 26004558 NA 4.20E-06