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 mr1761 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
vg1016528653 sf1016457426 10 16528653 4.96E-10 2.42E-06
vg0134771269 sf0134770226 1 34771269 6.45E-10 NA
vg1217552425 sf1217546380 12 17552425 6.66E-10 NA
vg0202764681 sf0202764679 2 2764681 2.66E-09 NA
vg0113850020 sf0113848994 1 13850020 3.37E-09 NA
vg0824858262 sf0824855548 8 24858262 3.71E-08 1.67E-06
vg1122505213 sf1122039084 11 22505213 1.60E-07 NA
vg0321406609 sf0321405119 3 21406609 1.35E-06 NA
vg0225359588 sf0225353719 2 25359588 1.41E-06 NA
vg1119658949 sf1119192637 11 19658949 NA 3.02E-06
vg1119648094 sf1119181782 11 19648094 NA 3.42E-06
vg1122529329 sf1122063200 11 22529329 NA 4.66E-06