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Detailed information for vg0918113312:

Variant ID: vg0918113312 (JBrowse)Variation Type: INDEL
Chromosome: chr09Position: 18113312
Reference Allele: TAlternative Allele: TA
Primary Allele: TSecondary Allele: TA

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


TATATAGAATTTGGAACACCTTGGCCCTCATTGGCTCATACTTGATATAGAAATTACTCTGTCATGGTATTTACCTTCTGCTTGTTGTTGCCATGAGAAA[T/TA]
AAAAAAAAATGGCAGTTAAATTCGTGCATTGCATTGTCATGTGCAGAGAAACAGAAATCCAAGTGCACGAACAGAAGATAAACAAATATCAAGCTATACT

Reverse complement sequence

AGTATAGCTTGATATTTGTTTATCTTCTGTTCGTGCACTTGGATTTCTGTTTCTCTGCACATGACAATGCAATGCACGAATTTAACTGCCATTTTTTTTT[A/TA]
TTTCTCATGGCAACAACAAGCAGAAGGTAAATACCATGACAGAGTAATTTCTATATCAAGTATGAGCCAATGAGGGCCAAGGTGTTCCAAATTCTATATA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of TA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.20% 7.40% 0.36% 0.00% NA
All Indica  2759 86.80% 12.60% 0.58% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 64.00% 34.30% 1.68% 0.00% NA
Indica II  465 97.00% 3.00% 0.00% 0.00% NA
Indica III  913 98.90% 1.10% 0.00% 0.00% NA
Indica Intermediate  786 83.80% 15.40% 0.76% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 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 96.70% 2.20% 1.11% 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
vg0918113312 T -> TA LOC_Os09g29790.1 upstream_gene_variant ; 4000.0bp to feature; MODIFIER silent_mutation Average:36.525; most accessible tissue: Callus, score: 71.857 N N N N
vg0918113312 T -> TA LOC_Os09g29810.1 upstream_gene_variant ; 1812.0bp to feature; MODIFIER silent_mutation Average:36.525; most accessible tissue: Callus, score: 71.857 N N N N
vg0918113312 T -> TA LOC_Os09g29800.1 intron_variant ; MODIFIER silent_mutation Average:36.525; most accessible tissue: Callus, score: 71.857 N N N N