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 mr1958 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
vg1118831958 sf1118365766 11 18831958 3.11E-10 NA
vg1118828056 sf1118361864 11 18828056 3.25E-10 4.87E-07
vg0329034942 sf0329027994 3 29034942 2.33E-09 NA
vg0912965190 sf0912964189 9 12965190 5.08E-09 NA
vg1119207316 sf1118741004 11 19207316 6.64E-09 NA
vg0500738633 sf0500738633 5 738633 7.58E-09 NA
vg1222863485 sf1222829925 12 22863485 1.32E-06 NA
vg0303013101 sf0303012097 3 3013101 NA 1.11E-06
vg1203735286 sf1203734285 12 3735286 NA 4.41E-06