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Detailed information for vg1123253227:

Variant ID: vg1123253227 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 23253227
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGAACGCCAGGATGGAGTCGACGTACCCCTGCGCCAATAATGGCGCAACGGCGGCTGGCTTCTGCGGCTCGCCGGCGGCGGTGGCGGCCGCCGCCGCCGT[C/T]
GTCTTCTTTGCCTCGTCGGCTGATGCCACCGCAGAGGCGTCCATGGATGATGGATCAGTATTCACTTGGAGTGCGTATGTCGACGAACTCGGTTGCTTGT

Reverse complement sequence

ACAAGCAACCGAGTTCGTCGACATACGCACTCCAAGTGAATACTGATCCATCATCCATGGACGCCTCTGCGGTGGCATCAGCCGACGAGGCAAAGAAGAC[G/A]
ACGGCGGCGGCGGCCGCCACCGCCGCCGGCGAGCCGCAGAAGCCAGCCGCCGTTGCGCCATTATTGGCGCAGGGGTACGTCGACTCCATCCTGGCGTTCG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.90% 2.10% 0.02% 0.00% NA
All Indica  2759 99.60% 0.40% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 69.50% 30.50% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.10% 0.90% 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 96.90% 2.10% 1.04% 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
vg1123253227 C -> T LOC_Os11g39060.1 synonymous_variant ; p.Thr15Thr; LOW synonymous_codon Average:69.551; most accessible tissue: Callus, score: 82.581 N N N N