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Detailed information for vg1105159777:

Variant ID: vg1105159777 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 5159777
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGCTCGAAGGGCCGCGCGCCACCTTCGCTCTTCCAAGTAGCCGAGGTCAGGGAGCGTCGGCTTCCTTCTTTTTGTCGCTCGCAGGCCTCCCCTTTCGGGT[G/A]
GCCAGCGAAACGCCTTCGACGGCGAGGACATGACCCTCGTCGTCGGAATGGGCTGACCTCTTCTTCCTCCTCCTGTCACGCCGCCCTGTCCGAGCAGCAG

Reverse complement sequence

CTGCTGCTCGGACAGGGCGGCGTGACAGGAGGAGGAAGAAGAGGTCAGCCCATTCCGACGACGAGGGTCATGTCCTCGCCGTCGAAGGCGTTTCGCTGGC[C/T]
ACCCGAAAGGGGAGGCCTGCGAGCGACAAAAAGAAGGAAGCCGACGCTCCCTGACCTCGGCTACTTGGAAGAGCGAAGGTGGCGCGCGGCCCTTCGAGCC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 40.80% 0.10% 25.35% 33.81% NA
All Indica  2759 17.40% 0.00% 35.56% 47.01% NA
All Japonica  1512 86.20% 0.00% 6.02% 7.74% NA
Aus  269 14.90% 0.00% 35.69% 49.44% NA
Indica I  595 14.10% 0.00% 16.47% 69.41% NA
Indica II  465 6.50% 0.00% 30.75% 62.80% NA
Indica III  913 18.30% 0.00% 57.50% 24.21% NA
Indica Intermediate  786 25.40% 0.00% 27.35% 47.20% NA
Temperate Japonica  767 90.00% 0.00% 1.69% 8.34% NA
Tropical Japonica  504 82.70% 0.00% 10.52% 6.75% NA
Japonica Intermediate  241 81.70% 0.00% 10.37% 7.88% NA
VI/Aromatic  96 61.50% 3.10% 17.71% 17.71% NA
Intermediate  90 47.80% 0.00% 14.44% 37.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1105159777 G -> A LOC_Os11g09660.1 synonymous_variant ; p.Ala448Ala; LOW synonymous_codon Average:5.323; most accessible tissue: Callus, score: 10.907 N N N N
vg1105159777 G -> DEL LOC_Os11g09660.1 N frameshift_variant Average:5.323; most accessible tissue: Callus, score: 10.907 N N N N