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 mr1698 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
vg0200805927 sf0200805927 2 805927 8.28E-09 NA
vg0140816254 sf0140815211 1 40816254 1.26E-08 NA
vg0101289411 sf0101288411 1 1289411 1.59E-08 NA
vg0223818027 sf0223812158 2 23818027 1.77E-08 NA
vg0121174382 sf0121173337 1 21174382 4.67E-08 4.59E-06
vg0121624043 sf0121622998 1 21624043 1.13E-06 2.17E-06
vg1118205187 sf1117739045 11 18205187 2.73E-06 NA