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Detailed information for vg0108457498:

Variant ID: vg0108457498 (JBrowse)Variation Type: INDEL
Chromosome: chr01Position: 8457498
Reference Allele: CAAAlternative Allele: C
Primary Allele: CAASecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAGGAGGACAGGGGGAGAGACAACCACCATGAAAGTGAAAGACACCCATGACAATCAACACACGCCTACCAGAAGCCACAACATACAAGCCTACATACGC[CAA/C]
GACACGCCGCCGGATATCGACTTGAAGGATAGGCATGGCTATTCCCCTACGGTGTCTCCGGATACCGTCAGGAGATACGAAAGCGCTATCTCTGATCTCG

Reverse complement sequence

CGAGATCAGAGATAGCGCTTTCGTATCTCCTGACGGTATCCGGAGACACCGTAGGGGAATAGCCATGCCTATCCTTCAAGTCGATATCCGGCGGCGTGTC[TTG/G]
GCGTATGTAGGCTTGTATGTTGTGGCTTCTGGTAGGCGTGTGTTGATTGTCATGGGTGTCTTTCACTTTCATGGTGGTTGTCTCTCCCCCTGTCCTCCTA

Allele Frequencies:

Populations Population SizeFrequency of CAA(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.80% 7.20% 0.04% 0.00% NA
All Indica  2759 96.30% 3.70% 0.07% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 14.10% 85.90% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 97.60% 2.40% 0.00% 0.00% NA
Indica III  913 95.20% 4.80% 0.00% 0.00% NA
Indica Intermediate  786 93.90% 5.90% 0.25% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0108457498 CAA -> C LOC_Os01g15070.1 frameshift_variant ; p.Gln25fs; HIGH frameshift_variant Average:57.83; most accessible tissue: Minghui63 young leaf, score: 70.655 N N N N