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 mr1551 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
vg0713522827 sf0713521834 7 13522827 7.73E-11 NA
vg1011512074 sf1011440893 10 11512074 7.79E-11 NA
vg1011512457 sf1011441276 10 11512457 1.53E-10 4.12E-06
vg0311279294 sf0311278012 3 11279294 2.27E-10 NA
vg0410306276 sf0410296974 4 10306276 2.77E-10 NA
vg1215438530 sf1215435828 12 15438530 3.99E-10 9.51E-06
vg0503991118 sf0503991095 5 3991118 1.15E-08 NA
vg1007488823 sf1007504446 10 7488823 1.52E-07 NA