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Detailed information for vg0503844538:

Variant ID: vg0503844538 (JBrowse)Variation Type: INDEL
Chromosome: chr05Position: 3844538
Reference Allele: TTTCAlternative Allele: T
Primary Allele: TTTCSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CAAGAATATATGATCTTCCTAGTAATGGTGCTCAAAAGAGATATATATATCGAGCACAAATTAGGGGAAACACCTTTAAACTCTCAAGAAATATCCCTCC[TTTC/T]
CTCAGACACCATCCAAACATCCAAACAGTTATGAAAAAAGTCTCAATTTTTTTTACAATATTCATACAACATACATATACCACTTCATAAAATCCTAAGG

Reverse complement sequence

CCTTAGGATTTTATGAAGTGGTATATGTATGTTGTATGAATATTGTAAAAAAAATTGAGACTTTTTTCATAACTGTTTGGATGTTTGGATGGTGTCTGAG[GAAA/A]
GGAGGGATATTTCTTGAGAGTTTAAAGGTGTTTCCCCTAATTTGTGCTCGATATATATATCTCTTTTGAGCACCATTACTAGGAAGATCATATATTCTTG

Allele Frequencies:

Populations Population SizeFrequency of TTTC(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.70% 0.30% 0.00% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 95.50% 4.50% 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  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 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 98.90% 1.10% 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
vg0503844538 TTTC -> T LOC_Os05g07260.1 downstream_gene_variant ; 1370.0bp to feature; MODIFIER silent_mutation Average:38.065; most accessible tissue: Callus, score: 80.816 N N N N
vg0503844538 TTTC -> T LOC_Os05g07260.2 downstream_gene_variant ; 1381.0bp to feature; MODIFIER silent_mutation Average:38.065; most accessible tissue: Callus, score: 80.816 N N N N
vg0503844538 TTTC -> T LOC_Os05g07260.4 downstream_gene_variant ; 1381.0bp to feature; MODIFIER silent_mutation Average:38.065; most accessible tissue: Callus, score: 80.816 N N N N
vg0503844538 TTTC -> T LOC_Os05g07260.3 downstream_gene_variant ; 1370.0bp to feature; MODIFIER silent_mutation Average:38.065; most accessible tissue: Callus, score: 80.816 N N N N
vg0503844538 TTTC -> T LOC_Os05g07270.1 intron_variant ; MODIFIER silent_mutation Average:38.065; most accessible tissue: Callus, score: 80.816 N N N N