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 mr1445 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
vg1114806383 sf1114342697 11 14806383 9.75E-07 9.75E-07
vg0513518841 sf0513461388 5 13518841 1.05E-06 1.06E-06
vg0103538854 sf0103537854 1 3538854 2.52E-06 2.52E-06
vg0225285799 sf0225279930 2 25285799 3.14E-06 3.14E-06
vg0226921378 sf0226915509 2 26921378 4.25E-06 4.25E-06
vg1215925567 sf1215922863 12 15925567 6.44E-06 6.44E-06