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 mr1086 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
vg0719051231 sf0719050238 7 19051231 1.15E-14 8.44E-16
vg0719039736 sf0719038743 7 19039736 1.49E-14 9.18E-17
vg0719040385 sf0719039392 7 19040385 3.38E-14 1.55E-16
vg0719156501 sf0719155508 7 19156501 8.87E-11 5.47E-11
vg0719125702 sf0719124709 7 19125702 8.88E-11 2.39E-11
vg0719141838 sf0719140845 7 19141838 3.37E-09 2.99E-10
vg0817806989 sf0817804276 8 17806989 1.40E-06 3.13E-07
vg1101911438 sf1101910439 11 1911438 2.51E-06 2.27E-06
vg0811122650 sf0811121655 8 11122650 NA 1.99E-07
vg0408184131 sf0408179405 4 8184131 NA 2.34E-06
vg0418079489 sf0417907530 4 18079489 NA 4.36E-06