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 mr1316 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
vg0700146376 sf0700145376 7 146376 7.42E-10 8.05E-07
vg0700121974 sf0700120974 7 121974 8.86E-10 5.96E-07
vg0700072352 sf0700071352 7 72352 9.80E-10 6.27E-07
vg0114251394 sf0114250368 1 14251394 1.54E-06 2.28E-06
vg0114276377 sf0114275351 1 14276377 1.79E-06 2.13E-06