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 mr1879 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
vg0714952310 sf0714951317 7 14952310 1.59E-06 NA
vg0313966137 sf0313964854 3 13966137 5.00E-06 1.49E-06
vg0307393257 sf0307392255 3 7393257 NA 2.35E-06
vg0622756910 sf0622755913 6 22756910 NA 4.77E-06
vg1218108461 sf1218079897 12 18108461 NA 7.12E-06