Additional file 3: of High-specificity detection of rare alleles with Paired-End Low Error Sequencing (PELE-Seq)

SNP-calling results from E. coli spike-in libraries using the PELE-Seq, ORP, and Standard DNA-Seq methods. The performance of the PELE-Seq, ORP, and standard DNA-Seq methods at detecting rare alleles at various read depths. SNP results for spike-in libraries 1–4 are reported, as well as read depths and other metrics for the libraries. Various allele frequency and quality score cutoffs were tested to optimize rare variant identification with the method, and the SNP-calling results are reported here. Recommended workflow and SNP-calling parameters are reported here and in Additional file 6. (XLSX 54 kb)