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Detailed information for vg0823066434:

Variant ID: vg0823066434 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 23066434
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCGGCCCGTCGAGGTTCTCCTACTGCCTCACGTCGTTCCTCTCGCCGGAGCCGAGCCGGCTCAACTTCGGCGTGTTCGCGACGCTCAACGGCACCAACGC[A/C]
AGCTCCTCCGGCTCGCCGGTGCAGTCCACGCCGCTGGTCGTCAACGCGGCGCTGCCGTCCCTCTACTTCATGTCCCTCAAGGGCATCAGCCTCGGCCAGA

Reverse complement sequence

TCTGGCCGAGGCTGATGCCCTTGAGGGACATGAAGTAGAGGGACGGCAGCGCCGCGTTGACGACCAGCGGCGTGGACTGCACCGGCGAGCCGGAGGAGCT[T/G]
GCGTTGGTGCCGTTGAGCGTCGCGAACACGCCGAAGTTGAGCCGGCTCGGCTCCGGCGAGAGGAACGACGTGAGGCAGTAGGAGAACCTCGACGGGCCGA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.50% 2.50% 0.00% 0.00% NA
All Indica  2759 99.30% 0.70% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 63.90% 36.10% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 98.90% 1.10% 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 97.90% 2.10% 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
vg0823066434 A -> C LOC_Os08g36530.1 synonymous_variant ; p.Ala267Ala; LOW synonymous_codon Average:72.431; most accessible tissue: Zhenshan97 flower, score: 81.325 N N N N