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Detailed information for vg0215134812:

Variant ID: vg0215134812 (JBrowse)Variation Type: INDEL
Chromosome: chr02Position: 15134812
Reference Allele: ACAlternative Allele: A
Primary Allele: ACSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCGTATCCACCCCGCCCGTGGCGAAACGCGTGCGCCTTTTTGGAGTCTACATCGACGTTCCTCCACTGCGCCCAGGCGGCGAGGCAACACAAGATTTCA[AC/A]
CCATGATGATGGCGTGCCATCCGTGGACAGGAACGCCCTCAAGAGGAGGCGAGCTGCTGCGGACAATTAACGCCTCCTGATCGAATTGTATCGTTTAGAT

Reverse complement sequence

ATCTAAACGATACAATTCGATCAGGAGGCGTTAATTGTCCGCAGCAGCTCGCCTCCTCTTGAGGGCGTTCCTGTCCACGGATGGCACGCCATCATCATGG[GT/T]
TGAAATCTTGTGTTGCCTCGCCGCCTGGGCGCAGTGGAGGAACGTCGATGTAGACTCCAAAAAGGCGCACGCGTTTCGCCACGGGCGGGGTGGATACGAG

Allele Frequencies:

Populations Population SizeFrequency of AC(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.60% 2.40% 0.00% 0.00% NA
All Indica  2759 98.20% 1.80% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 75.50% 24.50% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 98.00% 2.00% 0.00% 0.00% NA
Indica Intermediate  786 96.60% 3.40% 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  90 100.00% 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
vg0215134812 AC -> A LOC_Os02g25830.1 frameshift_variant ; p.Pro272fs; HIGH frameshift_variant Average:77.885; most accessible tissue: Zhenshan97 young leaf, score: 85.001 N N N N