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 mr1115 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
vg0604294396 sf0604293397 6 4294396 7.43E-28 1.51E-10
vg0604304747 sf0604303748 6 4304747 2.03E-24 1.80E-09
vg0432212638 sf0432027530 4 32212638 6.16E-22 NA
vg0604308260 sf0604307261 6 4308260 9.91E-20 1.03E-10
vg0805092111 sf0805091114 8 5092111 1.87E-19 NA
vg0140053429 sf0140052386 1 40053429 2.39E-19 NA
vg0604300121 sf0604299122 6 4300121 2.57E-19 5.59E-07
vg0327080189 sf0327073242 3 27080189 2.72E-19 NA
vg0433037993 sf0432852880 4 33037993 NA 7.94E-07