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 mr1161 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
vg0420116884 sf0419944922 4 20116884 2.94E-08 NA
vg0805000244 sf0804999247 8 5000244 4.15E-08 NA
vg0141861461 sf0141860418 1 41861461 4.57E-08 NA
vg1226817020 sf1226783419 12 26817020 6.27E-08 NA
vg0709675339 sf0709674345 7 9675339 6.40E-08 6.00E-06
vg0709672762 sf0709671768 7 9672762 1.11E-07 2.85E-06
vg0308368499 sf0308367437 3 8368499 7.58E-06 NA