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 mr1853 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
vg1004654643 sf1004671180 10 4654643 2.53E-08 2.53E-08
vg1213118008 sf1213115347 12 13118008 1.96E-07 1.96E-07
vg1004256106 sf1004272644 10 4256106 8.82E-07 8.82E-07
vg1214093173 sf1214090513 12 14093173 2.18E-06 2.18E-06
vg0628687836 sf0628686838 6 28687836 2.32E-06 2.32E-06
vg0128742019 sf0128740974 1 28742019 4.71E-06 4.71E-06
vg0715983729 sf0715982736 7 15983729 6.96E-06 6.96E-06