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 mr1788 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
vg0414209075 sf0414199791 4 14209075 5.01E-09 4.61E-06
vg0314648455 sf0314647142 3 14648455 8.87E-09 NA
vg1124179798 sf1123713668 11 24179798 9.60E-09 NA
vg0314622952 sf0314621639 3 14622952 1.66E-08 NA
vg1100779104 sf1100778105 11 779104 4.13E-08 NA
vg0709436324 sf0709435330 7 9436324 7.52E-08 NA
vg0400103899 sf0400102899 4 103899 1.22E-07 3.55E-06
vg0325133506 sf0325131587 3 25133506 1.88E-06 4.84E-06
vg0201553858 sf0201553858 2 1553858 6.27E-06 NA
vg1003719342 sf1003718319 10 3719342 NA 2.74E-06