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 mr1407 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
vg0407833565 sf0407828833 4 7833565 3.14E-08 2.07E-07
vg0813739257 sf0813736543 8 13739257 1.86E-07 1.85E-06
vg0318146978 sf0318145760 3 18146978 2.42E-07 3.21E-06
vg1125707575 sf1125241414 11 25707575 NA 2.53E-06
vg1117597342 sf1117131199 11 17597342 NA 2.95E-06