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 mr1246 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
vg0719055987 sf0719054994 7 19055987 8.29E-20 1.79E-15
vg0722044007 sf0722043014 7 22044007 2.92E-09 NA
vg0901474384 sf0901473384 9 1474384 1.92E-08 6.21E-06
vg0111260241 sf0111259217 1 11260241 2.15E-08 NA
vg0809713528 sf0809712532 8 9713528 2.46E-08 NA
vg0725004532 sf0725003538 7 25004532 8.70E-08 2.48E-06
vg0626882641 sf0626881644 6 26882641 7.34E-07 3.29E-06
vg0719053396 sf0719052403 7 19053396 NA 4.76E-06