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 mr1965 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
vg0704864945 sf0704863946 7 4864945 9.55E-07 9.55E-07
vg0614715408 sf0614714409 6 14715408 1.18E-06 1.18E-06
vg0421020772 sf0420848825 4 21020772 3.12E-06 3.12E-06
vg0607659813 sf0607658814 6 7659813 4.18E-06 4.18E-06
vg0501795080 sf0501795063 5 1795080 4.70E-06 4.70E-06
vg0424181194 sf0423996055 4 24181194 5.49E-06 5.49E-06
vg0501807498 sf0501807481 5 1807498 5.73E-06 5.73E-06