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 mr1663 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
vg0105180474 sf0105179474 1 5180474 3.36E-13 NA
vg0105188247 sf0105187247 1 5188247 4.53E-13 NA
vg0429470009 sf0429284878 4 29470009 1.12E-12 NA
vg0717156727 sf0717155734 7 17156727 1.93E-12 4.23E-06
vg0122033482 sf0122032437 1 22033482 5.33E-12 NA
vg0704519293 sf0704518294 7 4519293 6.36E-12 NA
vg0600909609 sf0600908610 6 909609 NA 2.68E-06