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 mr1323 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
vg0104000380 sf0103999380 1 4000380 2.10E-21 1.62E-08
vg0907071077 sf0907070077 9 7071077 1.88E-19 NA
vg1002049340 sf1002048317 10 2049340 3.82E-19 NA
vg0230976585 sf0230970716 2 30976585 5.13E-19 NA
vg1119446198 sf1118979886 11 19446198 6.52E-19 NA
vg0917850917 sf0917849916 9 17850917 5.38E-18 NA
vg0208268939 sf0208268938 2 8268939 NA 8.64E-08
vg1226056282 sf1226022676 12 26056282 NA 1.38E-07
vg1215673774 sf1215671071 12 15673774 NA 3.66E-07
vg1218087584 sf1218059020 12 18087584 NA 6.34E-06