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 mr1668 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
vg1125636908 sf1125170747 11 25636908 1.51E-12 9.60E-06
vg0401742334 sf0401737933 4 1742334 9.77E-12 NA
vg0141748081 sf0141747038 1 41748081 1.18E-11 NA
vg1013420246 sf1013349016 10 13420246 1.74E-11 NA
vg0207187961 sf0207187961 2 7187961 2.12E-11 NA
vg1117693473 sf1117227329 11 17693473 4.11E-11 NA
vg1126179984 sf1125708398 11 26179984 3.58E-08 2.65E-06
vg1126180021 sf1125708435 11 26180021 9.35E-08 6.76E-06
vg1012949570 sf1012878385 10 12949570 NA 6.23E-08
vg0700410899 sf0700409899 7 410899 NA 1.52E-06
vg0429616201 sf0429431068 4 29616201 NA 3.92E-06