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Detailed information for vg0121350108:

Variant ID: vg0121350108 (JBrowse)Variation Type: INDEL
Chromosome: chr01Position: 21350108
Reference Allele: TGAlternative Allele: T
Primary Allele: TGSecondary Allele: T

Inferred Ancestral Allele : TG (evidence from allele frequency in Oryza rufipogon: TG: 1.00, T: 0.00, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


TGGCTTTGCGAAGTGGACCGTTCAAGAGGCGCCTGGGGAACGGTTTGATTGGCTGGAAATGAAGGGGTTCTACTGCTGCGAGGCACAAGGTGCGTATAGT[TG/T]
AAAAGAGTAAAAAGGTACACAACTGCAAAAATCAGCTCGGTCTACAACCGCTTAAAATTACGTTCCGTCCTTATATATAGATTCATTTGTTTCTACCTTA

Reverse complement sequence

TAAGGTAGAAACAAATGAATCTATATATAAGGACGGAACGTAATTTTAAGCGGTTGTAGACCGAGCTGATTTTTGCAGTTGTGTACCTTTTTACTCTTTT[CA/A]
ACTATACGCACCTTGTGCCTCGCAGCAGTAGAACCCCTTCATTTCCAGCCAATCAAACCGTTCCCCAGGCGCCTCTTGAACGGTCCACTTCGCAAAGCCA

Allele Frequencies:

Populations Population SizeFrequency of TG(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.70% 1.20% 0.02% 0.00% NA
All Indica  2759 98.90% 1.10% 0.00% 0.00% NA
All Japonica  1512 98.30% 1.70% 0.07% 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 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 96.30% 3.70% 0.00% 0.00% NA
Temperate Japonica  767 96.60% 3.30% 0.13% 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 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0121350108 TG -> T LOC_Os01g38120.1 upstream_gene_variant ; 435.0bp to feature; MODIFIER silent_mutation Average:75.691; most accessible tissue: Zhenshan97 root, score: 83.751 N N N N
vg0121350108 TG -> T LOC_Os01g38140.1 upstream_gene_variant ; 4361.0bp to feature; MODIFIER silent_mutation Average:75.691; most accessible tissue: Zhenshan97 root, score: 83.751 N N N N
vg0121350108 TG -> T LOC_Os01g38130.1 intron_variant ; MODIFIER silent_mutation Average:75.691; most accessible tissue: Zhenshan97 root, score: 83.751 N N N N