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Detailed information for vg0138754197:

Variant ID: vg0138754197 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 38754197
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.01, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


AGGTTGAGCTCTTGAAGGGCAAGTTTGGATTTGATGCAGCTTTCAACTATAAAGAGGAGCCTGACTTGACTGCAGCCTTGAAAAGGTCAGGCCTTCTCTT[T/C]
CAGTTAAAAGGCACGGCTTAATTTAGGTTCAATGAGCAATTGATGAATTAAGATAGATTATAACGATCATCTAAAAATCTTAATTAAAATACTGCAATAG

Reverse complement sequence

CTATTGCAGTATTTTAATTAAGATTTTTAGATGATCGTTATAATCTATCTTAATTCATCAATTGCTCATTGAACCTAAATTAAGCCGTGCCTTTTAACTG[A/G]
AAGAGAAGGCCTGACCTTTTCAAGGCTGCAGTCAAGTCAGGCTCCTCTTTATAGTTGAAAGCTGCATCAAATCCAAACTTGCCCTTCAAGAGCTCAACCT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.00% 2.00% 0.00% 0.00% NA
All Indica  2759 99.60% 0.40% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 74.00% 26.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.30% 0.70% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.60% 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 88.50% 11.50% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0138754197 T -> C LOC_Os01g66710.1 downstream_gene_variant ; 3429.0bp to feature; MODIFIER silent_mutation Average:53.174; most accessible tissue: Callus, score: 85.066 N N N N
vg0138754197 T -> C LOC_Os01g66730.1 downstream_gene_variant ; 861.0bp to feature; MODIFIER silent_mutation Average:53.174; most accessible tissue: Callus, score: 85.066 N N N N
vg0138754197 T -> C LOC_Os01g66730.2 downstream_gene_variant ; 889.0bp to feature; MODIFIER silent_mutation Average:53.174; most accessible tissue: Callus, score: 85.066 N N N N
vg0138754197 T -> C LOC_Os01g66720.1 intron_variant ; MODIFIER silent_mutation Average:53.174; most accessible tissue: Callus, score: 85.066 N N N N