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 mr1839 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
vg0205296507 sf0205296506 2 5296507 8.18E-14 4.29E-08
vg0205296566 sf0205296565 2 5296566 1.89E-13 4.24E-08
vg0129497686 sf0129496641 1 29497686 1.88E-12 4.07E-06
vg0132158418 sf0132157374 1 32158418 5.00E-12 7.35E-06
vg1117584893 sf1117118750 11 17584893 8.63E-12 2.06E-07
vg0135718510 sf0135717467 1 35718510 1.69E-10 NA
vg1126694376 sf1126222763 11 26694376 4.22E-08 8.87E-07
vg1217609308 sf1217603263 12 17609308 2.08E-06 NA