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 mr1192 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
vg0900843348 sf0900842348 9 843348 5.39E-08 5.39E-08
vg0805005643 sf0805004646 8 5005643 1.19E-07 1.19E-07
vg0610852582 sf0610851583 6 10852582 1.29E-07 1.29E-07
vg0321576069 sf0321574579 3 21576069 2.38E-07 2.38E-07
vg0222337580 sf0222331711 2 22337580 3.39E-07 3.39E-07
vg0107079035 sf0107078035 1 7079035 1.93E-06 1.93E-06