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 mr1568 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
vg0419536798 sf0419364836 4 19536798 8.88E-12 3.14E-07
vg0116188975 sf0116187949 1 16188975 2.54E-10 4.63E-07
vg0135062105 sf0135061062 1 35062105 4.76E-10 1.33E-06
vg0912106235 sf0912105234 9 12106235 1.01E-09 NA
vg0100999668 sf0100998668 1 999668 1.33E-09 NA
vg1216116414 sf1216113710 12 16116414 NA 2.98E-06
vg1209407906 sf1209405315 12 9407906 NA 3.81E-06