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 mr1863 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
vg0222723138 sf0222717269 2 22723138 8.63E-14 4.96E-13
vg0222725941 sf0222720072 2 22725941 9.87E-14 4.87E-13
vg0217838858 sf0217832989 2 17838858 1.61E-09 8.88E-09
vg1214822308 sf1214819649 12 14822308 2.41E-08 8.87E-07
vg0224274080 sf0224268211 2 24274080 4.87E-08 7.54E-06
vg0334893672 sf0334886542 3 34893672 3.33E-06 3.56E-06
vg0115899007 sf0115897981 1 15899007 NA 4.59E-06