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 mr1593 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
vg0507088705 sf0507088647 5 7088705 3.62E-76 1.78E-44
vg0619720091 sf0619719094 6 19720091 2.15E-17 NA
vg0506565714 sf0506565655 5 6565714 1.52E-14 8.45E-07
vg0507368901 sf0507368844 5 7368901 3.51E-14 2.22E-06
vg0705394646 sf0705393647 7 5394646 2.67E-13 NA
vg0507156565 sf0507156507 5 7156565 5.87E-11 2.37E-07
vg0507335771 sf0507335713 5 7335771 1.17E-10 1.03E-12
vg0303346069 sf0303345065 3 3346069 3.19E-10 7.95E-07
vg0508324298 sf0508324226 5 8324298 5.59E-10 1.18E-07
vg0510456115 sf0510459274 5 10456115 3.56E-09 4.14E-07
vg0506971537 sf0506971479 5 6971537 6.87E-09 9.65E-07
vg0513100366 sf0513043288 5 13100366 8.76E-09 1.30E-07