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
vg0912814461 sf0912813460 9 12814461 7.76E-33 2.36E-07
vg0235871188 sf0235865319 2 35871188 1.22E-30 NA
vg0726269098 sf0726268104 7 26269098 2.22E-30 NA
vg0127415010 sf0127413966 1 27415010 2.47E-30 NA
vg0721643942 sf0721642949 7 21643942 2.55E-30 NA
vg0907362663 sf0907361663 9 7362663 2.44E-29 3.05E-06
vg0314826271 sf0314824958 3 14826271 NA 2.28E-06