Search for Variation information by Variation ID:

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

Detailed information for vg0409081384:

Variant ID: vg0409081384 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 9081384
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.61, A: 0.39, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


GTGAGAGGAGCAGGTGATGGCGGTGACCATCGTGGGAGGAGCAGGAGATGGCAGCAACGCTCCGTGGTGCTGGTGGGGAGATCTTCTGGCAACGACGGCA[G/A]
TGCTCGCGAGCACGCGTGGATTCGACGAGGGTGGCTGCGGCGACGCTCGCGGACGCATTGGGGGTGACAGCAGCACTCGCGGGCACATCCAACAATGGTG

Reverse complement sequence

CACCATTGTTGGATGTGCCCGCGAGTGCTGCTGTCACCCCCAATGCGTCCGCGAGCGTCGCCGCAGCCACCCTCGTCGAATCCACGCGTGCTCGCGAGCA[C/T]
TGCCGTCGTTGCCAGAAGATCTCCCCACCAGCACCACGGAGCGTTGCTGCCATCTCCTGCTCCTCCCACGATGGTCACCGCCATCACCTGCTCCTCTCAC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 65.00% 35.00% 0.04% 0.00% NA
All Indica  2759 98.90% 1.00% 0.04% 0.00% NA
All Japonica  1512 1.10% 98.90% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 98.20% 1.70% 0.13% 0.00% NA
Temperate Japonica  767 0.50% 99.50% 0.00% 0.00% NA
Tropical Japonica  504 1.40% 98.60% 0.00% 0.00% NA
Japonica Intermediate  241 2.10% 97.90% 0.00% 0.00% NA
VI/Aromatic  96 14.60% 85.40% 0.00% 0.00% NA
Intermediate  90 48.90% 50.00% 1.11% 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
vg0409081384 G -> A LOC_Os04g16690.1 synonymous_variant ; p.Gln18Gln; LOW synonymous_codon Average:70.641; most accessible tissue: Zhenshan97 young leaf, score: 87.153 N N N N