Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1202830847:

Variant ID: vg1202830847 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 2830847
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: 0.02, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:


AGAATGGTCTCCATGAAGAGGTATTGTGTTTATTTCAGAGTACACAAAGGGAAGGAATGCAATTGACTGAATTCACTGTTTCATCTATCCTCAGCACATG[T/C]
GCAAGCTTAGCATTGATAATTGAAGGAACACAGGTGCATGCAGTTATTGTTAAGCATGGTTTTCATAGGAACCTCTTTGTAGCAACATCTCTTGTGGATG

Reverse complement sequence

CATCCACAAGAGATGTTGCTACAAAGAGGTTCCTATGAAAACCATGCTTAACAATAACTGCATGCACCTGTGTTCCTTCAATTATCAATGCTAAGCTTGC[A/G]
CATGTGCTGAGGATAGATGAAACAGTGAATTCAGTCAATTGCATTCCTTCCCTTTGTGTACTCTGAAATAAACACAATACCTCTTCATGGAGACCATTCT

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 97.30% 2.60% 0.04% 0.00% NA
All Indica  2759 99.00% 1.00% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 64.70% 34.60% 0.74% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 99.50% 0.50% 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 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg1202830847 T -> C LOC_Os12g06070.1 synonymous_variant ; p.Cys268Cys; LOW synonymous_codon Average:46.896; most accessible tissue: Zhenshan97 young leaf, score: 67.83 N N N N