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 mr1603 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
vg0217411971 sf0217406101 2 17411971 7.24E-08 1.28E-06
vg1004292753 sf1004309291 10 4292753 1.12E-07 2.96E-06
vg0217096193 sf0217090323 2 17096193 2.04E-07 6.85E-07
vg0100619688 sf0100618688 1 619688 2.25E-07 NA
vg0516132563 sf0516075047 5 16132563 4.71E-07 2.85E-07
vg0719728155 sf0719727162 7 19728155 2.84E-06 8.71E-06
vg1214628048 sf1214625388 12 14628048 8.77E-06 3.75E-06
vg1121619789 sf1121153666 11 21619789 NA 1.42E-06
vg0121402829 sf0121401784 1 21402829 NA 3.86E-06