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 mr1790 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
vg1018813458 sf1018742015 10 18813458 1.83E-14 NA
vg0301118906 sf0301117904 3 1118906 3.09E-13 NA
vg0228486603 sf0228480734 2 28486603 5.83E-13 NA
vg1215671844 sf1215669141 12 15671844 7.09E-13 3.35E-06
vg1220866478 sf1220833027 12 20866478 7.78E-13 NA
vg1215673774 sf1215671071 12 15673774 2.24E-12 9.16E-07
vg1119594595 sf1119128283 11 19594595 1.81E-11 3.54E-07
vg0300033578 sf0300032578 3 33578 4.52E-10 NA
vg1107270469 sf1107266214 11 7270469 NA 1.88E-06
vg0900146158 sf0900145158 9 146158 NA 3.56E-06