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Detailed information for vg0222979755:

Variant ID: vg0222979755 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 22979755
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, C: 0.05, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:


TGATTTGTTTCTGTCATTTTCTGTGGTTATCGATCGCCAACCTGCAAAACCTGCATTGCGTTGCGCGGTTGCGTTCGCGGATCACGAGTTCACGTCGTTT[C/G]
AGATTTAGAAATTAGAAGAACTGTTCGTCCGATCCGGGGAATTCGGGTGATAGGGAGATTTGTTATGTTTTGCATTTCTCGGGTAGTTTTTCAGTCCAGA

Reverse complement sequence

TCTGGACTGAAAAACTACCCGAGAAATGCAAAACATAACAAATCTCCCTATCACCCGAATTCCCCGGATCGGACGAACAGTTCTTCTAATTTCTAAATCT[G/C]
AAACGACGTGAACTCGTGATCCGCGAACGCAACCGCGCAACGCAATGCAGGTTTTGCAGGTTGGCGATCGATAACCACAGAAAATGACAGAAACAAATCA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.50% 4.50% 0.00% 0.00% NA
All Indica  2759 97.50% 2.50% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 48.70% 51.30% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.30% 1.70% 0.00% 0.00% NA
Indica III  913 95.70% 4.30% 0.00% 0.00% NA
Indica Intermediate  786 97.30% 2.70% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 0.00% 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
vg0222979755 C -> G LOC_Os02g38029.1 upstream_gene_variant ; 3119.0bp to feature; MODIFIER silent_mutation Average:68.605; most accessible tissue: Callus, score: 87.432 N N N N
vg0222979755 C -> G LOC_Os02g38020.1 downstream_gene_variant ; 4459.0bp to feature; MODIFIER silent_mutation Average:68.605; most accessible tissue: Callus, score: 87.432 N N N N
vg0222979755 C -> G LOC_Os02g38050.1 downstream_gene_variant ; 2091.0bp to feature; MODIFIER silent_mutation Average:68.605; most accessible tissue: Callus, score: 87.432 N N N N
vg0222979755 C -> G LOC_Os02g38020.2 downstream_gene_variant ; 4459.0bp to feature; MODIFIER silent_mutation Average:68.605; most accessible tissue: Callus, score: 87.432 N N N N
vg0222979755 C -> G LOC_Os02g38050.4 downstream_gene_variant ; 2078.0bp to feature; MODIFIER silent_mutation Average:68.605; most accessible tissue: Callus, score: 87.432 N N N N
vg0222979755 C -> G LOC_Os02g38050.3 downstream_gene_variant ; 2078.0bp to feature; MODIFIER silent_mutation Average:68.605; most accessible tissue: Callus, score: 87.432 N N N N
vg0222979755 C -> G LOC_Os02g38050.5 downstream_gene_variant ; 2078.0bp to feature; MODIFIER silent_mutation Average:68.605; most accessible tissue: Callus, score: 87.432 N N N N
vg0222979755 C -> G LOC_Os02g38050.6 downstream_gene_variant ; 2078.0bp to feature; MODIFIER silent_mutation Average:68.605; most accessible tissue: Callus, score: 87.432 N N N N
vg0222979755 C -> G LOC_Os02g38050.2 downstream_gene_variant ; 2091.0bp to feature; MODIFIER silent_mutation Average:68.605; most accessible tissue: Callus, score: 87.432 N N N N
vg0222979755 C -> G LOC_Os02g38040.1 intron_variant ; MODIFIER silent_mutation Average:68.605; most accessible tissue: Callus, score: 87.432 N N N N