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 mr1435 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
vg0216569039 sf0216563169 2 16569039 1.53E-16 4.67E-08
vg1018579412 sf1018507969 10 18579412 1.24E-14 2.63E-06
vg1219997122 sf1219968564 12 19997122 1.02E-13 NA
vg1018280719 sf1018209276 10 18280719 2.24E-13 2.37E-06
vg0720065275 sf0720064282 7 20065275 7.89E-13 NA
vg0905179424 sf0905178424 9 5179424 8.55E-13 NA