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Detailed information for vg1123252949:

Variant ID: vg1123252949 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 23252949
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCAATATCTCATGGCTACTCGAATTCGAAGGCGCTCCAGTCGATCTTGGCCCATTCTTCGTTGATCAGAGCCTCGAGCTTGGCCTGATCGGCGAGGTAG[C/T]
TCTCGCCGACGACGTAGCAGCCGTTGTCCTCGACCTGGCGGCTGACCTCGGCCTGGAACACGGCGAGGTCGTCGTCCAAAGCCTTGTGCAGGGCGGCCAT

Reverse complement sequence

ATGGCCGCCCTGCACAAGGCTTTGGACGACGACCTCGCCGTGTTCCAGGCCGAGGTCAGCCGCCAGGTCGAGGACAACGGCTGCTACGTCGTCGGCGAGA[G/A]
CTACCTCGCCGATCAGGCCAAGCTCGAGGCTCTGATCAACGAAGAATGGGCCAAGATCGACTGGAGCGCCTTCGAATTCGAGTAGCCATGAGATATTGAG

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 99.60% 0.40% 0.00% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 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 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 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
vg1123252949 C -> T LOC_Os11g39060.1 missense_variant ; p.Ser108Asn; MODERATE nonsynonymous_codon ; S108N Average:68.777; most accessible tissue: Callus, score: 83.174 unknown unknown DELETERIOUS 0.02