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Detailed information for vg0200790720:

Variant ID: vg0200790720 (JBrowse)Variation Type: INDEL
Chromosome: chr02Position: 790720
Reference Allele: GAlternative Allele: GAA,GA,GAAA
Primary Allele: GAASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:


AATGAGACAAAGATTTCATTTTTATTTAAGAACAAGTGAACAACTGATGAACTTTAGAGAGCTAGACTCTATGTACTGTAATGCTTTTGTTATTATTTTG[G/GAA,GA,GAAA]
AAAAAAAAGGGTGAGAATTCTTCCTTGGCTGGAATTTCAACTGGCCTAAGAATTGTGATCAAGCTAAGCTTGAACTAACCCAAAGCTAAGTACTCTCTGT

Reverse complement sequence

ACAGAGAGTACTTAGCTTTGGGTTAGTTCAAGCTTAGCTTGATCACAATTCTTAGGCCAGTTGAAATTCCAGCCAAGGAAGAATTCTCACCCTTTTTTTT[C/TTC,TC,TTTC]
CAAAATAATAACAAAAGCATTACAGTACATAGAGTCTAGCTCTCTAAAGTTCATCAGTTGTTCACTTGTTCTTAAATAAAAATGAAATCTTTGTCTCATT

Allele Frequencies:

Populations Population SizeFrequency of GAA(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.30% 37.60% 0.53% 0.00% GA: 7.45%; GAAA: 0.13%
All Indica  2759 86.70% 6.10% 0.36% 0.00% GA: 6.67%; GAAA: 0.18%
All Japonica  1512 5.70% 92.80% 0.60% 0.00% GA: 0.86%; GAAA: 0.07%
Aus  269 19.30% 24.90% 0.74% 0.00% GA: 55.02%
Indica I  595 98.20% 0.50% 0.84% 0.00% GAAA: 0.34%; GA: 0.17%
Indica II  465 70.50% 21.30% 0.43% 0.00% GA: 7.74%
Indica III  913 88.90% 1.40% 0.11% 0.00% GA: 9.31%; GAAA: 0.22%
Indica Intermediate  786 85.10% 6.60% 0.25% 0.00% GA: 7.89%; GAAA: 0.13%
Temperate Japonica  767 0.50% 97.10% 1.04% 0.00% GA: 1.30%
Tropical Japonica  504 10.10% 89.10% 0.20% 0.00% GA: 0.60%
Japonica Intermediate  241 12.90% 86.70% 0.00% 0.00% GAAA: 0.41%
VI/Aromatic  96 15.60% 83.30% 0.00% 0.00% GA: 1.04%
Intermediate  90 24.40% 64.40% 4.44% 0.00% GA: 6.67%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0200790720 G -> GAA LOC_Os02g02360.1 downstream_gene_variant ; 1486.0bp to feature; MODIFIER silent_mutation Average:60.317; most accessible tissue: Callus, score: 86.638 N N N N
vg0200790720 G -> GAA LOC_Os02g02380.1 downstream_gene_variant ; 4345.0bp to feature; MODIFIER silent_mutation Average:60.317; most accessible tissue: Callus, score: 86.638 N N N N
vg0200790720 G -> GAA LOC_Os02g02370.1 intron_variant ; MODIFIER silent_mutation Average:60.317; most accessible tissue: Callus, score: 86.638 N N N N
vg0200790720 G -> GA LOC_Os02g02360.1 downstream_gene_variant ; 1486.0bp to feature; MODIFIER silent_mutation Average:60.317; most accessible tissue: Callus, score: 86.638 N N N N
vg0200790720 G -> GA LOC_Os02g02380.1 downstream_gene_variant ; 4345.0bp to feature; MODIFIER silent_mutation Average:60.317; most accessible tissue: Callus, score: 86.638 N N N N
vg0200790720 G -> GA LOC_Os02g02370.1 intron_variant ; MODIFIER silent_mutation Average:60.317; most accessible tissue: Callus, score: 86.638 N N N N
vg0200790720 G -> GAAA LOC_Os02g02360.1 downstream_gene_variant ; 1486.0bp to feature; MODIFIER silent_mutation Average:60.317; most accessible tissue: Callus, score: 86.638 N N N N
vg0200790720 G -> GAAA LOC_Os02g02380.1 downstream_gene_variant ; 4345.0bp to feature; MODIFIER silent_mutation Average:60.317; most accessible tissue: Callus, score: 86.638 N N N N
vg0200790720 G -> GAAA LOC_Os02g02370.1 intron_variant ; MODIFIER silent_mutation Average:60.317; most accessible tissue: Callus, score: 86.638 N N N N