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Detailed information for vg1101692318:

Variant ID: vg1101692318 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 1692318
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCGAGAAGCTGGCGTGCAAGACGATCGCGAAGCGGAAGCTGGCGAACAAGGAGGACGTCGACGACGTCCGCCGCGAGGTGCAGATCATGCACCACCTCTC[C/T]
GGCCAGCCAAACATCGTCGACCTCCGCGGCGCCTACGAGGACAAGCACAACGTCCACCTCGTGATGGAGCTCTGCGCCGGCGGCGAGCTCTTCGACCGCA

Reverse complement sequence

TGCGGTCGAAGAGCTCGCCGCCGGCGCAGAGCTCCATCACGAGGTGGACGTTGTGCTTGTCCTCGTAGGCGCCGCGGAGGTCGACGATGTTTGGCTGGCC[G/A]
GAGAGGTGGTGCATGATCTGCACCTCGCGGCGGACGTCGTCGACGTCCTCCTTGTTCGCCAGCTTCCGCTTCGCGATCGTCTTGCACGCCAGCTTCTCGC

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% 0.02% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 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  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 58.30% 40.60% 1.04% 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
vg1101692318 C -> T LOC_Os11g04170.1 synonymous_variant ; p.Ser139Ser; LOW synonymous_codon Average:62.809; most accessible tissue: Zhenshan97 panicle, score: 77.482 N N N N