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 mr1417 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
vg0623833223 sf0623832226 6 23833223 8.24E-09 8.24E-09
vg1119956594 sf1119490517 11 19956594 4.21E-07 4.21E-07
vg1110436569 sf1110431114 11 10436569 9.81E-07 9.81E-07
vg0410080228 sf0410070926 4 10080228 1.09E-06 1.09E-06
vg0626887934 sf0626886937 6 26887934 1.36E-06 1.36E-06
vg0206906369 sf0206906369 2 6906369 2.40E-06 2.41E-06
vg1215686397 sf1215683694 12 15686397 2.47E-06 2.47E-06
vg0406862618 sf0406858063 4 6862618 4.00E-06 4.00E-06