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 mr1427 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
vg0124420479 sf0124419435 1 24420479 1.55E-07 1.55E-07
vg0500776377 sf0500776359 5 776377 4.68E-07 4.68E-07
vg0606109335 sf0606108336 6 6109335 7.19E-07 7.20E-07
vg0135190066 sf0135189023 1 35190066 8.61E-07 8.61E-07
vg0208626738 sf0208626737 2 8626738 1.93E-06 1.93E-06
vg0805005643 sf0805004646 8 5005643 3.09E-06 3.09E-06
vg0604014602 sf0604013603 6 4014602 3.71E-06 3.71E-06
vg1215225558 sf1215222855 12 15225558 7.68E-06 7.68E-06