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 mr1465 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
vg0608245933 sf0608244934 6 8245933 2.29E-13 NA
vg0621502460 sf0621501463 6 21502460 2.70E-13 NA
vg0402051312 sf0402046908 4 2051312 8.20E-13 NA
vg0107281602 sf0107280602 1 7281602 4.85E-12 NA
vg0141992653 sf0141991610 1 41992653 8.02E-12 7.16E-07
vg1203011971 sf1203010973 12 3011971 1.06E-09 NA