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 mr1162 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
vg0800542399 sf0800541399 8 542399 6.50E-11 NA
vg0111937827 sf0111936801 1 11937827 6.10E-10 NA
vg0524300403 sf0524237822 5 24300403 6.64E-10 NA
vg0407785574 sf0407780842 4 7785574 6.93E-10 NA
vg0518492960 sf0518432446 5 18492960 1.14E-09 NA
vg0420830218 sf0420658261 4 20830218 1.77E-09 8.08E-06
vg0801342227 sf0801341229 8 1342227 2.04E-09 NA
vg1112898481 sf1112434802 11 12898481 4.03E-09 2.71E-06
vg0900528417 sf0900527417 9 528417 8.47E-09 NA
vg0500056395 sf0500056395 5 56395 NA 1.68E-06