Search for Variation information by Variation ID:

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

Detailed information for vg0905621013:

Variant ID: vg0905621013 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 5621013
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, A: 0.01, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


GCCTTGCGTCGAAGCGAAGAGATGGATCTTCTTCCTCTGGAATAGCTGGCTCTCTTTCTTCTGGATCTTCCTCCTCTGGGGTAGCTGACGGCGGTGCTTC[T/A]
CCCTTGAGCTCGGCCAGTTCCTTCTGCAGGCGATACACCTTGCTTTCTAGCTTGCAAATCTTGCGACGGTTCCAATTTTCCCTCTCATGAGCTGCTTTCC

Reverse complement sequence

GGAAAGCAGCTCATGAGAGGGAAAATTGGAACCGTCGCAAGATTTGCAAGCTAGAAAGCAAGGTGTATCGCCTGCAGAAGGAACTGGCCGAGCTCAAGGG[A/T]
GAAGCACCGCCGTCAGCTACCCCAGAGGAGGAAGATCCAGAAGAAAGAGAGCCAGCTATTCCAGAGGAAGAAGATCCATCTCTTCGCTTCGACGCAAGGC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.20% 1.80% 0.00% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 98.80% 1.20% 0.00% 0.00% NA
Aus  269 98.50% 1.50% 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 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.50% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 93.40% 6.60% 0.00% 0.00% NA
VI/Aromatic  96 46.90% 53.10% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0905621013 T -> A LOC_Os09g10310.1 synonymous_variant ; p.Gly172Gly; LOW nonsynonymous_codon ; G172V Average:53.91; most accessible tissue: Zhenshan97 flag leaf, score: 71.238 unknown unknown DELETERIOUS 0.00