Search for Variation information by Variation ID:

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

Detailed information for vg0517885916:

Variant ID: vg0517885916 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 17885916
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: 0.00, others allele: 0.00, population size: 322. )

Flanking Sequence (100 bp) in Reference Genome:


TCATCATGTCATCAAATAGCAGACATGCAATCAATTTTCATCTTCGCTACTTAAACAATGTGCTCCCAAGGGTGATGATGGCGGTTCCATCACCCATAAT[C/T]
GTTGTCAGAGACATCTCTGTCTCAAGAATTCTGTCTAGTTCTGTCGCGACTAACCTCATCTTTGGCCTTCTTCTTGAAGATGGAGTCAGGCACTGAAAGG

Reverse complement sequence

CCTTTCAGTGCCTGACTCCATCTTCAAGAAGAAGGCCAAAGATGAGGTTAGTCGCGACAGAACTAGACAGAATTCTTGAGACAGAGATGTCTCTGACAAC[G/A]
ATTATGGGTGATGGAACCGCCATCATCACCCTTGGGAGCACATTGTTTAAGTAGCGAAGATGAAAATTGATTGCATGTCTGCTATTTGATGACATGATGA

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 98.60% 1.40% 0.00% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 81.80% 18.20% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 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 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  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0517885916 C -> T LOC_Os05g30820.1 synonymous_variant ; p.Thr361Thr; LOW synonymous_codon Average:64.45; most accessible tissue: Zhenshan97 flower, score: 77.755 N N N N