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 mr1894 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
vg0105521069 sf0105520069 1 5521069 2.94E-09 NA
vg1217711180 sf1217705135 12 17711180 6.44E-09 NA
vg0132005816 sf0132004772 1 32005816 5.53E-08 NA
vg1125669886 sf1125203725 11 25669886 5.76E-07 9.38E-07
vg0102106039 sf0102105039 1 2106039 3.58E-06 NA
vg0232481318 sf0232475449 2 32481318 4.39E-06 2.20E-06
vg0316482661 sf0316481306 3 16482661 4.85E-06 NA
vg0820479378 sf0820476665 8 20479378 8.50E-06 NA
vg0434775337 sf0434590228 4 34775337 9.46E-06 6.53E-07
vg0818230180 sf0818227467 8 18230180 NA 3.59E-06
vg0101328049 sf0101327049 1 1328049 NA 8.22E-06