Abstract
This work explores the influence of several variables on stutter formation across sequenced autosomal STR loci (simple, compound, and complex motifs) and different alleles within each locus. The variables are sequence variations within the repeating motifs and flanking region [1,2]; longest uninterrupted stretch (LUS) [3]; parental allele length [3]; and base pair content and length value of each repeating motif from which the stutter has generated [3,4]. Over six hundred unrelated individuals from different populations were amplified with the prototype PowerSeq 46GY System and sequenced on the Illumina MiSeq platform. Raw FASTQ files were analyzed with STRait Razor v3 [5]. Stutter ratio was calculated for motifs that exhibited stutter using the ratio of the observed coverage of the stutter sequence at (N-1) position to the observed coverage of the allelic sequence. Understanding the behavior (abundance, reproducibility, sequence context) of non-allelic artifacts will help in establishing probabilistic models for the prediction of stutter rate and interpretation of sequence-based STR profiles.
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