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 mr1814 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
vg0918774898 sf0918773898 9 18774898 3.24E-07 3.24E-07
vg0220479392 sf0220473524 2 20479392 6.99E-07 6.99E-07
vg0805108529 sf0805107532 8 5108529 7.21E-07 7.22E-07
vg1214703763 sf1214701104 12 14703763 2.08E-06 2.08E-06
vg1014073653 sf1014002419 10 14073653 2.32E-06 2.32E-06
vg0207698155 sf0207698154 2 7698155 3.45E-06 3.45E-06
vg0305129097 sf0305128099 3 5129097 3.95E-06 3.96E-06