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 mr1971 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
vg0404490479 sf0404486083 4 4490479 4.45E-09 5.07E-07
vg1217636564 sf1217630519 12 17636564 4.66E-09 NA
vg0138112582 sf0138111539 1 38112582 1.30E-08 NA
vg0526986295 sf0526923651 5 26986295 1.80E-08 NA
vg0113507299 sf0113506273 1 13507299 2.16E-08 NA
vg0225867144 sf0225861275 2 25867144 5.62E-08 3.47E-06
vg0608669135 sf0608668136 6 8669135 9.15E-07 2.90E-06
vg0724902343 sf0724901349 7 24902343 1.72E-06 3.13E-06
vg0616217404 sf0616216406 6 16217404 2.13E-06 NA