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 mr1772 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
vg0604300121 sf0604299122 6 4300121 1.23E-08 7.11E-08
vg1223454241 sf1223420701 12 23454241 4.33E-08 2.80E-07
vg1222484865 sf1222451304 12 22484865 9.86E-08 2.98E-06
vg1223453821 sf1223420281 12 23453821 1.35E-07 6.16E-07
vg0420190623 sf0420018663 4 20190623 7.63E-07 2.39E-06
vg1217812137 sf1217783571 12 17812137 3.52E-06 2.72E-06
vg1002941211 sf1002940188 10 2941211 5.68E-06 2.52E-06
vg0220720577 sf0220714709 2 20720577 7.05E-06 1.84E-06
vg1226056282 sf1226022676 12 26056282 NA 7.56E-07