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Detailed information for vg0522746655:

Variant ID: vg0522746655 (JBrowse)Variation Type: INDEL
Chromosome: chr05Position: 22746655
Reference Allele: TGCAlternative Allele: T
Primary Allele: TGCSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTAGCCGATGATGTCGACGAGGTTGTCGTGGTGGAGCCGGCTGAGCTTCGAGACCTCGTCCAGGAACTCATTGTTGCCTTGGAAGCCATGCCTGTCCAGC[TGC/T]
TTGATGACCACGGTCTGATCATGCACAAAAAAACAAAGAAAAAACATAATTAGTTCTTGTTTATGCGAAGTGATCACTGCGCTGCTCGATGAAATAGATG

Reverse complement sequence

CATCTATTTCATCGAGCAGCGCAGTGATCACTTCGCATAAACAAGAACTAATTATGTTTTTTCTTTGTTTTTTTGTGCATGATCAGACCGTGGTCATCAA[GCA/A]
GCTGGACAGGCATGGCTTCCAAGGCAACAATGAGTTCCTGGACGAGGTCTCGAAGCTCAGCCGGCTCCACCACGACAACCTCGTCGACATCATCGGCTAC

Allele Frequencies:

Populations Population SizeFrequency of TGC(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.60% 0.10% 0.23% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 98.80% 0.50% 0.73% 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  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 97.70% 0.90% 1.43% 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  90 100.00% 0.00% 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
vg0522746655 TGC -> T LOC_Os05g38770.1 frameshift_variant ; p.Gln111fs; HIGH frameshift_variant Average:58.883; most accessible tissue: Zhenshan97 young leaf, score: 76.44 N N N N