Search for Variation information by Variation ID:

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

Detailed information for vg1224819153:

Variant ID: vg1224819153 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 24819153
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 345. )

Flanking Sequence (100 bp) in Reference Genome:


TAAAGAAGCAAGACACTTTCTCACAGCCACTTGCATCAAAGATTAGTACATCAAAGGAGAAGCTGCCATTGCAACGGCCATTGCAAGTGAAGAACAGGAG[G/A]
TCATTCTCCTGCAATTCATGAGCCTTGGCAAAATCCTCCCATCCTGACATGAGGATCAGCTCATCAGCAACCTTTTCGACGCTGACACGCCATGTTTCGC

Reverse complement sequence

GCGAAACATGGCGTGTCAGCGTCGAAAAGGTTGCTGATGAGCTGATCCTCATGTCAGGATGGGAGGATTTTGCCAAGGCTCATGAATTGCAGGAGAATGA[C/T]
CTCCTGTTCTTCACTTGCAATGGCCGTTGCAATGGCAGCTTCTCCTTTGATGTACTAATCTTTGATGCAAGTGGCTGTGAGAAAGTGTCTTGCTTCTTTA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.90% 0.10% 0.02% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 97.40% 2.20% 0.37% 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  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 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  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 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
vg1224819153 G -> A LOC_Os12g40120.1 synonymous_variant ; p.Asp98Asp; LOW synonymous_codon Average:50.335; most accessible tissue: Zhenshan97 panicle, score: 73.605 N N N N