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Detailed information for vg1212722721:

Variant ID: vg1212722721 (JBrowse)Variation Type: INDEL
Chromosome: chr12Position: 12722721
Reference Allele: TGAlternative Allele: T
Primary Allele: TGSecondary Allele: Unkown

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTAACCGTGCCAACCACAAGCCAGCGTAGGCAACGGCTTTACCTTTTGTATAGCATGATTCATTACGGGGTGCCAGACTGATAAGCGGTGAGAAGTCCG[TG/T]
GGGGTCGCTGGGGAGTCCATGCCTCTGGTTATATTTATAGAGGGGGTGATTATGATCCAGGAATGGTGCACTATGGTGAGTTGTGTTGTGCAGGGGGTAC

Reverse complement sequence

GTACCCCCTGCACAACACAACTCACCATAGTGCACCATTCCTGGATCATAATCACCCCCTCTATAAATATAACCAGAGGCATGGACTCCCCAGCGACCCC[CA/A]
CGGACTTCTCACCGCTTATCAGTCTGGCACCCCGTAATGAATCATGCTATACAAAAGGTAAAGCCGTTGCCTACGCTGGCTTGTGGTTGGCACGGTTAAT

Allele Frequencies:

Populations Population SizeFrequency of TG(primary allele) Frequency of Unkown(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.50% 0.00% 0.04% 0.49% NA
All Indica  2759 100.00% 0.00% 0.00% 0.04% NA
All Japonica  1512 98.40% 0.00% 0.13% 1.46% 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 99.90% 0.00% 0.00% 0.13% NA
Temperate Japonica  767 97.40% 0.00% 0.13% 2.48% NA
Tropical Japonica  504 99.80% 0.00% 0.00% 0.20% NA
Japonica Intermediate  241 98.80% 0.00% 0.41% 0.83% 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
vg1212722721 TG -> T LOC_Os12g22540.1 frameshift_variant ; p.Val29fs; HIGH N Average:55.863; most accessible tissue: Minghui63 young leaf, score: 78.054 N N N N