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 mr1183 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
vg0910805763 sf0910804762 9 10805763 2.10E-12 NA
vg0528575652 sf0528513007 5 28575652 1.34E-11 NA
vg0106218065 sf0106217065 1 6218065 1.91E-11 NA
vg0807399839 sf0807398844 8 7399839 3.26E-11 NA
vg1204514412 sf1204513400 12 4514412 3.83E-11 NA
vg0106106067 sf0106105067 1 6106067 6.80E-09 NA
vg0906700489 sf0906699489 9 6700489 5.84E-08 3.06E-06
vg0704734352 sf0704733353 7 4734352 8.21E-07 NA
vg0714025862 sf0714024869 7 14025862 NA 1.66E-06
vg1121178330 sf1120712208 11 21178330 NA 2.84E-06