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 mr1878 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
vg0719011406 sf0719010413 7 19011406 5.79E-45 2.66E-10
vg0719199004 sf0719198011 7 19199004 1.03E-42 1.31E-17
vg0626675544 sf0626674547 6 26675544 8.29E-42 7.80E-06
vg0708048876 sf0708047881 7 8048876 1.01E-41 5.87E-06
vg0704640725 sf0704639726 7 4640725 2.41E-41 NA
vg0917092123 sf0917091122 9 17092123 1.01E-40 NA
vg0626871396 sf0626870399 6 26871396 2.22E-40 1.43E-06
vg0707881452 sf0707880457 7 7881452 1.43E-39 NA
vg0719091461 sf0719090468 7 19091461 NA 4.69E-13
vg0719181533 sf0719180540 7 19181533 NA 2.65E-08
vg0719198361 sf0719197368 7 19198361 NA 2.17E-07
vg0719208981 sf0719207988 7 19208981 NA 2.36E-07
vg0719466615 sf0719465622 7 19466615 NA 3.14E-07
vg0719065396 sf0719064403 7 19065396 NA 3.16E-07
vg0719618102 sf0719617109 7 19618102 NA 1.02E-06
vg0718985959 sf0718984966 7 18985959 NA 2.22E-06
vg0315179060 sf0315177707 3 15179060 NA 2.46E-06
vg0315219970 sf0315218617 3 15219970 NA 2.54E-06
vg0113087370 sf0113086344 1 13087370 NA 3.74E-06
vg0305833332 sf0305832332 3 5833332 NA 3.96E-06
vg0616962436 sf0616961439 6 16962436 NA 4.56E-06
vg0828393303 sf0828390589 8 28393303 NA 4.64E-06