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Detailed information for vg1123253199:

Variant ID: vg1123253199 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 23253199
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCGGAGAAGACCGGCCATTGCACCCTCTCGAACGCCAGGATGGAGTCGACGTACCCCTGCGCCAATAATGGCGCAACGGCGGCTGGCTTCTGCGGCTCGC[C/T]
GGCGGCGGTGGCGGCCGCCGCCGCCGTCGTCTTCTTTGCCTCGTCGGCTGATGCCACCGCAGAGGCGTCCATGGATGATGGATCAGTATTCACTTGGAGT

Reverse complement sequence

ACTCCAAGTGAATACTGATCCATCATCCATGGACGCCTCTGCGGTGGCATCAGCCGACGAGGCAAAGAAGACGACGGCGGCGGCGGCCGCCACCGCCGCC[G/A]
GCGAGCCGCAGAAGCCAGCCGCCGTTGCGCCATTATTGGCGCAGGGGTACGTCGACTCCATCCTGGCGTTCGAGAGGGTGCAATGGCCGGTCTTCTCCGA

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 99.00% 1.00% 0.00% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 96.90% 3.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 94.10% 5.90% 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  96 100.00% 0.00% 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
vg1123253199 C -> T LOC_Os11g39060.1 missense_variant ; p.Gly25Ser; MODERATE nonsynonymous_codon ; G25S Average:69.645; most accessible tissue: Callus, score: 82.581 unknown unknown TOLERATED 0.19