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 mr1738 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
vg0619381858 sf0619380861 6 19381858 5.67E-08 4.69E-06
vg1222349292 sf1222315731 12 22349292 3.49E-07 3.21E-07
vg1222400637 sf1222367076 12 22400637 6.94E-07 4.97E-06
vg1218065256 sf1218036692 12 18065256 1.27E-06 2.18E-06
vg0620348476 sf0620347479 6 20348476 2.16E-06 3.06E-06
vg0217863794 sf0217857925 2 17863794 2.23E-06 NA
vg0100948930 sf0100947930 1 948930 NA 2.96E-06
vg1214702209 sf1214699550 12 14702209 NA 5.75E-06