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 mr1298 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
vg0117668024 sf0117666978 1 17668024 4.44E-32 NA
vg0117162013 sf0117160967 1 17162013 1.18E-31 NA
vg0501598017 sf0501598001 5 1598017 3.48E-31 NA
vg0607145417 sf0607144418 6 7145417 3.73E-31 NA
vg0305498399 sf0305497399 3 5498399 5.04E-31 NA
vg0922482857 sf0922482376 9 22482857 7.11E-31 NA
vg1100781807 sf1100780808 11 781807 3.30E-28 1.55E-06
vg0800302779 sf0800301779 8 302779 NA 1.16E-06
vg1103943350 sf1103939252 11 3943350 NA 1.33E-06
vg0613088863 sf0613087864 6 13088863 NA 1.74E-06