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 mr1346 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
vg0724460006 sf0724459012 7 24460006 1.08E-10 NA
vg0315250257 sf0315248904 3 15250257 2.38E-10 NA
vg0124389643 sf0124388599 1 24389643 2.49E-10 NA
vg0618926527 sf0618925530 6 18926527 3.05E-10 NA
vg0728454407 sf0728453415 7 28454407 4.35E-10 NA
vg1213276842 sf1213274180 12 13276842 2.86E-07 NA
vg0909282800 sf0909281799 9 9282800 3.63E-07 NA
vg1011569110 sf1011497929 10 11569110 1.60E-06 NA
vg0619806827 sf0619805830 6 19806827 5.29E-06 NA
vg0315377711 sf0315376358 3 15377711 8.04E-06 NA
vg0805619517 sf0805618520 8 5619517 NA 3.78E-07
vg1215706891 sf1215704188 12 15706891 NA 3.87E-06
vg0122939348 sf0122938304 1 22939348 NA 4.68E-06
vg0107647091 sf0107646091 1 7647091 NA 7.79E-06