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Detailed information for vg0603899937:

Variant ID: vg0603899937 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 3899937
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TACTTTAAGCATGATTTATATCTTATACATTTACATAAATTTTTTAAATAAGACGAATGGTTAAACATGTATAAGTTAATGGTGTCACTTATTAAAAAAA[C/T]
AGAAGGAGTAATTAATAAGTGTGTGCGTGACTAGGAGTCAAAAACGGGATCTTGAGGTGGACTCCACACACACCACTAGGAGTCAAGCGTAGCTCCAAAA

Reverse complement sequence

TTTTGGAGCTACGCTTGACTCCTAGTGGTGTGTGTGGAGTCCACCTCAAGATCCCGTTTTTGACTCCTAGTCACGCACACACTTATTAATTACTCCTTCT[G/A]
TTTTTTTAATAAGTGACACCATTAACTTATACATGTTTAACCATTCGTCTTATTTAAAAAATTTATGTAAATGTATAAGATATAAATCATGCTTAAAGTA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.10% 1.40% 1.48% 0.00% NA
All Indica  2759 95.20% 2.40% 2.36% 0.00% NA
All Japonica  1512 99.80% 0.00% 0.20% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 84.20% 8.40% 7.39% 0.00% NA
Indica II  465 98.90% 0.00% 1.08% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 95.80% 2.20% 2.04% 0.00% NA
Temperate Japonica  767 99.70% 0.00% 0.26% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 0.00% 2.22% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0603899937 C -> T LOC_Os06g08060.1 upstream_gene_variant ; 551.0bp to feature; MODIFIER silent_mutation Average:45.512; most accessible tissue: Callus, score: 90.275 N N N N
vg0603899937 C -> T LOC_Os06g08032.1 downstream_gene_variant ; 4537.0bp to feature; MODIFIER silent_mutation Average:45.512; most accessible tissue: Callus, score: 90.275 N N N N
vg0603899937 C -> T LOC_Os06g08041.1 downstream_gene_variant ; 1152.0bp to feature; MODIFIER silent_mutation Average:45.512; most accessible tissue: Callus, score: 90.275 N N N N
vg0603899937 C -> T LOC_Os06g08070.1 downstream_gene_variant ; 3745.0bp to feature; MODIFIER silent_mutation Average:45.512; most accessible tissue: Callus, score: 90.275 N N N N
vg0603899937 C -> T LOC_Os06g08041-LOC_Os06g08060 intergenic_region ; MODIFIER silent_mutation Average:45.512; most accessible tissue: Callus, score: 90.275 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0603899937 NA 8.17E-06 mr1740 Ind_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0603899937 NA 2.01E-07 mr1864_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251