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 mr1159 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
vg0709448532 sf0709447538 7 9448532 7.43E-09 4.22E-08
vg0715403959 sf0715402966 7 15403959 2.11E-08 NA
vg0716100091 sf0716099098 7 16100091 8.43E-07 2.33E-06
vg0717352217 sf0717351224 7 17352217 9.81E-07 3.86E-06
vg0113749398 sf0113748372 1 13749398 NA 4.98E-06