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 mr1240 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
vg0817970097 sf0817967384 8 17970097 2.12E-08 2.12E-08
vg0222726032 sf0222720163 2 22726032 5.18E-07 5.18E-07
vg0222712682 sf0222706813 2 22712682 7.85E-07 7.85E-07
vg0402256940 sf0402252535 4 2256940 3.62E-06 3.62E-06
vg0601268839 sf0601267840 6 1268839 4.38E-06 4.38E-06
vg1107380267 sf1107376012 11 7380267 4.75E-06 4.75E-06
vg0324319095 sf0324317174 3 24319095 7.01E-06 7.02E-06