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Detailed information for vg0222980472:

Variant ID: vg0222980472 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 22980472
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:


GCCTCAAGATCCTCGACGTCTCGGGCAACAAGCTGAGGTCTCTCCCCGACAGCATCTCAAAATGCAGGTAGAATCAACCAGCCAAGGCCAAAGCACGCAT[C/T]
ATCATCATCTTCTTCTTCTCCCCAATGGCATCCAGATCCAGTTAAAGAAACTTCAATTCTCGCTAATGGTGATCATCACAAAATGATCCAAACGTACAGG

Reverse complement sequence

CCTGTACGTTTGGATCATTTTGTGATGATCACCATTAGCGAGAATTGAAGTTTCTTTAACTGGATCTGGATGCCATTGGGGAGAAGAAGAAGATGATGAT[G/A]
ATGCGTGCTTTGGCCTTGGCTGGTTGATTCTACCTGCATTTTGAGATGCTGTCGGGGAGAGACCTCAGCTTGTTGCCCGAGACGTCGAGGATCTTGAGGC

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 96.70% 3.30% 0.00% 0.00% NA
All Indica  2759 98.80% 1.20% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 54.30% 45.70% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 99.10% 0.90% 0.00% 0.00% NA
Indica Intermediate  786 97.70% 2.30% 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 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0222980472 C -> T LOC_Os02g38029.1 upstream_gene_variant ; 3836.0bp to feature; MODIFIER silent_mutation Average:81.77; most accessible tissue: Callus, score: 87.013 N N N N
vg0222980472 C -> T LOC_Os02g38050.1 downstream_gene_variant ; 1374.0bp to feature; MODIFIER silent_mutation Average:81.77; most accessible tissue: Callus, score: 87.013 N N N N
vg0222980472 C -> T LOC_Os02g38050.4 downstream_gene_variant ; 1361.0bp to feature; MODIFIER silent_mutation Average:81.77; most accessible tissue: Callus, score: 87.013 N N N N
vg0222980472 C -> T LOC_Os02g38050.3 downstream_gene_variant ; 1361.0bp to feature; MODIFIER silent_mutation Average:81.77; most accessible tissue: Callus, score: 87.013 N N N N
vg0222980472 C -> T LOC_Os02g38050.5 downstream_gene_variant ; 1361.0bp to feature; MODIFIER silent_mutation Average:81.77; most accessible tissue: Callus, score: 87.013 N N N N
vg0222980472 C -> T LOC_Os02g38050.6 downstream_gene_variant ; 1361.0bp to feature; MODIFIER silent_mutation Average:81.77; most accessible tissue: Callus, score: 87.013 N N N N
vg0222980472 C -> T LOC_Os02g38050.2 downstream_gene_variant ; 1374.0bp to feature; MODIFIER silent_mutation Average:81.77; most accessible tissue: Callus, score: 87.013 N N N N
vg0222980472 C -> T LOC_Os02g38040.1 intron_variant ; MODIFIER silent_mutation Average:81.77; most accessible tissue: Callus, score: 87.013 N N N N