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Detailed information for vg0708359170:

Variant ID: vg0708359170 (JBrowse)Variation Type: INDEL
Chromosome: chr07Position: 8359170
Reference Allele: GAlternative Allele: GGC
Primary Allele: GSecondary Allele: GGC

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGACGAAGGTGGGCTGGCGGACGAAGCCGAACGCGGAGATGAGCACGGCGAGGAGGAGGGTGCCAAAGACGATGCCGCACACGATGAGCCCGTCCCTACA[G/GGC]
TTGTTGCTGCAGGTGCAGCAGCACTCGTCGCACATTGTCGCCGCCGTCGTCGCGAGCGAGCGCTCGCCGGAATCGTTGCCGGTGGTGAGAGCTGGCTTGG

Reverse complement sequence

CCAAGCCAGCTCTCACCACCGGCAACGATTCCGGCGAGCGCTCGCTCGCGACGACGGCGGCGACAATGTGCGACGAGTGCTGCTGCACCTGCAGCAACAA[C/GCC]
TGTAGGGACGGGCTCATCGTGTGCGGCATCGTCTTTGGCACCCTCCTCCTCGCCGTGCTCATCTCCGCGTTCGGCTTCGTCCGCCAGCCCACCTTCGTCG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of GGC(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.60% 2.40% 0.04% 0.00% NA
All Indica  2759 96.80% 3.20% 0.04% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.50% 0.30% 0.17% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 99.20% 0.80% 0.00% 0.00% NA
Indica Intermediate  786 91.00% 9.00% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 78.10% 20.80% 1.04% 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
vg0708359170 G -> GGC LOC_Os07g14660.1 frameshift_variant ; p.Asn12fs; HIGH frameshift_variant Average:77.422; most accessible tissue: Zhenshan97 young leaf, score: 86.852 N N N N