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 mr1241 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
vg1201535323 sf1201534323 12 1535323 2.37E-09 7.51E-07
vg0327982584 sf0327975638 3 27982584 7.47E-09 NA
vg0707494583 sf0707493588 7 7494583 1.85E-08 NA
vg0719345307 sf0719344314 7 19345307 2.66E-08 9.36E-06
vg0619886817 sf0619885820 6 19886817 2.86E-08 NA
vg0604303058 sf0604302059 6 4303058 6.54E-08 2.41E-06
vg0719001862 sf0719000869 7 19001862 7.03E-08 7.17E-07
vg0608479610 sf0608478611 6 8479610 9.43E-08 NA
vg0608710017 sf0608709018 6 8710017 1.74E-07 3.44E-06
vg0717342657 sf0717341664 7 17342657 1.33E-06 1.85E-06
vg1112983207 sf1112519528 11 12983207 NA 6.76E-07