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 mr1170 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
vg0205949239 sf0205949239 2 5949239 1.97E-11 3.65E-07
vg1214693299 sf1214690638 12 14693299 2.48E-10 NA
vg0913468642 sf0913467641 9 13468642 3.41E-10 NA
vg0205949832 sf0205949832 2 5949832 6.66E-10 8.55E-07
vg0723948342 sf0723947348 7 23948342 2.08E-09 1.51E-06
vg0205414722 sf0205414722 2 5414722 3.39E-09 NA
vg0723950725 sf0723949731 7 23950725 3.60E-09 1.44E-06
vg0206231967 sf0206231967 2 6231967 1.06E-08 6.92E-08
vg0607995576 sf0607994577 6 7995576 1.41E-08 9.68E-06
vg1120196683 sf1119730605 11 20196683 3.03E-08 3.20E-06
vg0509797528 sf0509797457 5 9797528 2.42E-06 NA
vg0207854825 sf0207854824 2 7854825 NA 2.50E-06