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 mr1293 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
vg0220429795 sf0220423927 2 20429795 3.65E-08 3.65E-08
vg0220319668 sf0220313800 2 20319668 1.23E-07 1.23E-07
vg1213065934 sf1213063273 12 13065934 1.43E-06 1.43E-06
vg0314988402 sf0314987049 3 14988402 2.22E-06 2.22E-06
vg0905906905 sf0905905905 9 5906905 4.11E-06 4.11E-06
vg0515959945 sf0515902453 5 15959945 4.30E-06 4.30E-06