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Detailed information for vg0200562711:

Variant ID: vg0200562711 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 562711
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCTGTAACCCCCTTCTCAATCATACTCTTCATAACCCTGCTAGCAGTCTGAACCCGGCCACTGTTGAAAAGCGCTACCATGACAGACATGAACAGGGATG[G/A]
GCTCGGTACATGCCCTTGTTCCATCATACTGTCAAGTGCCGTCTTTGCATCAGCTGGCTCATTCTTCTTCAGGAAGCTATCAACAAGCAGTGCATGCGAT

Reverse complement sequence

ATCGCATGCACTGCTTGTTGATAGCTTCCTGAAGAAGAATGAGCCAGCTGATGCAAAGACGGCACTTGACAGTATGATGGAACAAGGGCATGTACCGAGC[C/T]
CATCCCTGTTCATGTCTGTCATGGTAGCGCTTTTCAACAGTGGCCGGGTTCAGACTGCTAGCAGGGTTATGAAGAGTATGATTGAGAAGGGGGTTACAGA

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 99.70% 0.20% 0.04% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 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 99.20% 0.70% 0.11% 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
vg0200562711 G -> A LOC_Os02g02020.1 missense_variant ; p.Pro566Ser; MODERATE N Average:73.691; most accessible tissue: Callus, score: 89.161 N N N N
vg0200562711 G -> A LOC_Os02g02010.1 downstream_gene_variant ; 2746.0bp to feature; MODIFIER N Average:73.691; most accessible tissue: Callus, score: 89.161 N N N N
vg0200562711 G -> A LOC_Os02g02030.1 downstream_gene_variant ; 2005.0bp to feature; MODIFIER N Average:73.691; most accessible tissue: Callus, score: 89.161 N N N N
vg0200562711 G -> A LOC_Os02g02040.1 downstream_gene_variant ; 3332.0bp to feature; MODIFIER N Average:73.691; most accessible tissue: Callus, score: 89.161 N N N N
vg0200562711 G -> A LOC_Os02g02040.4 downstream_gene_variant ; 3332.0bp to feature; MODIFIER N Average:73.691; most accessible tissue: Callus, score: 89.161 N N N N
vg0200562711 G -> A LOC_Os02g02040.6 downstream_gene_variant ; 3337.0bp to feature; MODIFIER N Average:73.691; most accessible tissue: Callus, score: 89.161 N N N N
vg0200562711 G -> A LOC_Os02g02040.3 downstream_gene_variant ; 3337.0bp to feature; MODIFIER N Average:73.691; most accessible tissue: Callus, score: 89.161 N N N N
vg0200562711 G -> A LOC_Os02g02040.2 downstream_gene_variant ; 3337.0bp to feature; MODIFIER N Average:73.691; most accessible tissue: Callus, score: 89.161 N N N N
vg0200562711 G -> A LOC_Os02g02040.5 downstream_gene_variant ; 3337.0bp to feature; MODIFIER N Average:73.691; most accessible tissue: Callus, score: 89.161 N N N N