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 mr1565 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
vg0401117842 sf0401113392 4 1117842 2.14E-21 2.27E-10
vg1207040173 sf1207039063 12 7040173 1.33E-16 NA
vg0106432168 sf0106431168 1 6432168 7.66E-16 NA
vg0400401937 sf0400400935 4 401937 1.79E-15 6.83E-07
vg0423160304 sf0422975159 4 23160304 1.75E-14 NA
vg1207212131 sf1207209525 12 7212131 3.56E-14 9.29E-07
vg1207251878 sf1207249285 12 7251878 5.55E-14 1.19E-06
vg0401819705 sf0401815300 4 1819705 7.23E-12 2.11E-06
vg0131535930 sf0131534886 1 31535930 1.61E-10 NA
vg0401256484 sf0401252034 4 1256484 NA 2.07E-06