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 mr1151 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
vg0724953161 sf0724952167 7 24953161 7.28E-14 NA
vg0920234916 sf0920234435 9 20234916 7.37E-14 NA
vg0132981769 sf0132980725 1 32981769 6.27E-13 NA
vg1200825909 sf1200824909 12 825909 1.50E-12 NA
vg0104020130 sf0104019130 1 4020130 2.36E-12 NA
vg0121835067 sf0121834022 1 21835067 7.59E-12 6.09E-07
vg0331870913 sf0331863790 3 31870913 3.55E-10 NA
vg1219745123 sf1219716593 12 19745123 3.12E-09 NA
vg0334983302 sf0334976172 3 34983302 NA 9.65E-09
vg0335111562 sf0335104432 3 35111562 NA 6.14E-08
vg0334550767 sf0334543637 3 34550767 NA 1.54E-07
vg0334366587 sf0334359457 3 34366587 NA 2.20E-07
vg0509971209 sf0509971138 5 9971209 NA 1.37E-06
vg0334582038 sf0334574908 3 34582038 NA 1.82E-06
vg0900280507 sf0900279507 9 280507 NA 2.41E-06
vg0334753499 sf0334746369 3 34753499 NA 3.44E-06