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 mr1842 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
vg0331248975 sf0331241860 3 31248975 1.25E-34 3.16E-21
vg0331280409 sf0331273294 3 31280409 5.54E-34 4.23E-21
vg1115503780 sf1115040093 11 15503780 3.98E-11 NA
vg0330599887 sf0330592776 3 30599887 5.98E-11 NA
vg0329556194 sf0329549234 3 29556194 2.64E-10 NA
vg0331359176 sf0331352061 3 31359176 2.70E-10 2.90E-08
vg0502198452 sf0502198427 5 2198452 1.25E-06 NA
vg1200595732 sf1200594732 12 595732 6.12E-06 7.86E-07
vg0201373773 sf0201373773 2 1373773 NA 4.26E-06
vg1124026214 sf1123560084 11 24026214 NA 4.46E-06