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Detailed information for vg0222979913:

Variant ID: vg0222979913 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 22979913
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: 313. )

Flanking Sequence (100 bp) in Reference Genome:


ATTTGTTATGTTTTGCATTTCTCGGGTAGTTTTTCAGTCCAGAAATGCAGATCGTATAAGACATTGCAGATGTGCATGCCCCAAAAATAATGGATGACGG[G/A]
TAGAACGCAATGCTGGTTAATTAAAATTGTCACTGAAAGCAATCCACTTATGAGTTAGGTTTATGAGAATTGTTTTTGCATTTTTTTTTTAAGATCACGC

Reverse complement sequence

GCGTGATCTTAAAAAAAAAATGCAAAAACAATTCTCATAAACCTAACTCATAAGTGGATTGCTTTCAGTGACAATTTTAATTAACCAGCATTGCGTTCTA[C/T]
CCGTCATCCATTATTTTTGGGGCATGCACATCTGCAATGTCTTATACGATCTGCATTTCTGGACTGAAAAACTACCCGAGAAATGCAAAACATAACAAAT

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 99.80% 0.10% 0.08% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 99.30% 0.40% 0.26% 0.00% NA
Aus  269 100.00% 0.00% 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  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 98.70% 0.80% 0.52% 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
vg0222979913 G -> A LOC_Os02g38029.1 upstream_gene_variant ; 3277.0bp to feature; MODIFIER N Average:56.315; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 N N N N
vg0222979913 G -> A LOC_Os02g38020.1 downstream_gene_variant ; 4617.0bp to feature; MODIFIER N Average:56.315; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 N N N N
vg0222979913 G -> A LOC_Os02g38050.1 downstream_gene_variant ; 1933.0bp to feature; MODIFIER N Average:56.315; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 N N N N
vg0222979913 G -> A LOC_Os02g38020.2 downstream_gene_variant ; 4617.0bp to feature; MODIFIER N Average:56.315; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 N N N N
vg0222979913 G -> A LOC_Os02g38050.4 downstream_gene_variant ; 1920.0bp to feature; MODIFIER N Average:56.315; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 N N N N
vg0222979913 G -> A LOC_Os02g38050.3 downstream_gene_variant ; 1920.0bp to feature; MODIFIER N Average:56.315; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 N N N N
vg0222979913 G -> A LOC_Os02g38050.5 downstream_gene_variant ; 1920.0bp to feature; MODIFIER N Average:56.315; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 N N N N
vg0222979913 G -> A LOC_Os02g38050.6 downstream_gene_variant ; 1920.0bp to feature; MODIFIER N Average:56.315; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 N N N N
vg0222979913 G -> A LOC_Os02g38050.2 downstream_gene_variant ; 1933.0bp to feature; MODIFIER N Average:56.315; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 N N N N
vg0222979913 G -> A LOC_Os02g38040.1 intron_variant ; MODIFIER N Average:56.315; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 N N N N