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 mr1398 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
vg0127041496 sf0127040452 1 27041496 4.48E-09 1.55E-06
vg1007906158 sf1007921768 10 7906158 8.13E-09 1.24E-06
vg0528889699 sf0528827054 5 28889699 1.42E-08 8.34E-06
vg0329508959 sf0329501999 3 29508959 1.64E-08 NA
vg1121157956 sf1120691835 11 21157956 1.86E-08 NA
vg1008204929 sf1008133791 10 8204929 5.43E-07 NA
vg1118275729 sf1117809588 11 18275729 6.48E-06 NA