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 mr1748 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
vg0125066238 sf0125065194 1 25066238 2.26E-07 2.26E-07
vg0416501266 sf0416329307 4 16501266 1.69E-06 1.69E-06
vg1221501463 sf1221468010 12 21501463 2.53E-06 2.53E-06
vg1005421909 sf1005438446 10 5421909 3.61E-06 3.61E-06
vg0620348476 sf0620347479 6 20348476 4.19E-06 4.19E-06
vg1204320877 sf1204319865 12 4320877 4.29E-06 4.29E-06
vg1018461662 sf1018390219 10 18461662 4.97E-06 4.97E-06