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Detailed information for vg0125056547:

Variant ID: vg0125056547 (JBrowse)Variation Type: INDEL
Chromosome: chr01Position: 25056547
Reference Allele: CAlternative Allele: CG
Primary Allele: CGSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 331. )

Flanking Sequence (100 bp) in Reference Genome:


GCCATGTGATTTAGTAATTTCAATATCATCTCTACATCTAAAAGATAACTTAAACATGGATTTCCTAAAAAAGTTACTTAATTTCAACATTTATTACTCA[C/CG]
GTTTTGAGTTTGCTCAGGCCTTCATAATCAAGTTTGTTTTTCTGAAATAGGCTTAGGACCTCCTCCCTTGCACGGTGCTGCCATTCTGGGTGCATGCTTA

Reverse complement sequence

TAAGCATGCACCCAGAATGGCAGCACCGTGCAAGGGAGGAGGTCCTAAGCCTATTTCAGAAAAACAAACTTGATTATGAAGGCCTGAGCAAACTCAAAAC[G/CG]
TGAGTAATAAATGTTGAAATTAAGTAACTTTTTTAGGAAATCCATGTTTAAGTTATCTTTTAGATGTAGAGATGATATTGAAATTACTAAATCACATGGC

Allele Frequencies:

Populations Population SizeFrequency of CG(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 75.70% 24.30% 0.00% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 27.70% 72.30% 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 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.60% 0.00% 0.00% NA
Temperate Japonica  767 3.10% 96.90% 0.00% 0.00% NA
Tropical Japonica  504 58.50% 41.50% 0.00% 0.00% NA
Japonica Intermediate  241 41.50% 58.50% 0.00% 0.00% NA
VI/Aromatic  96 76.00% 24.00% 0.00% 0.00% NA
Intermediate  90 74.40% 25.60% 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
vg0125056547 C -> CG LOC_Os01g43720.1 frameshift_variant&splice_region_variant ; p.???380fs; HIGH frameshift_variant Average:71.602; most accessible tissue: Callus, score: 90.679 N N N N