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 mr1517 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
vg0137838376 sf0137837333 1 37838376 2.51E-23 1.57E-21
vg0137838253 sf0137837210 1 37838253 5.62E-23 7.07E-22
vg0138431123 sf0138430080 1 38431123 1.56E-13 NA
vg0123684776 sf0123683732 1 23684776 5.88E-12 NA
vg1104987497 sf1104983308 11 4987497 8.73E-12 NA
vg0131229448 sf0131228404 1 31229448 9.71E-12 NA
vg0137745220 sf0137744177 1 37745220 3.14E-09 2.43E-08
vg0914575829 sf0914574828 9 14575829 5.67E-09 3.45E-06
vg0321862928 sf0321861438 3 21862928 3.69E-07 4.66E-06
vg0914571624 sf0914570623 9 14571624 3.93E-07 4.76E-06
vg0119648489 sf0119647444 1 19648489 9.11E-07 NA
vg0726547690 sf0726546696 7 26547690 1.83E-06 NA
vg0700414800 sf0700413800 7 414800 NA 4.82E-06