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 mr1972 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
vg1210731615 sf1210729028 12 10731615 2.80E-08 2.79E-08
vg0102116611 sf0102115611 1 2116611 8.53E-07 8.54E-07
vg0819855776 sf0819853063 8 19855776 1.15E-06 1.15E-06
vg0727126260 sf0727125266 7 27126260 1.71E-06 1.72E-06
vg1219554486 sf1219525956 12 19554486 1.87E-06 1.87E-06
vg0819497108 sf0819494395 8 19497108 2.57E-06 2.57E-06
vg1219662792 sf1219634262 12 19662792 2.62E-06 2.62E-06
vg0711419116 sf0711418122 7 11419116 3.24E-06 3.24E-06
vg0119388504 sf0119387459 1 19388504 3.50E-06 3.51E-06
vg1208280389 sf1208277795 12 8280389 4.79E-06 4.80E-06