Fig. 6

Evaluating sequence quality of bacterial FFPE DNA. a Evaluation of DNA sequence aberrations by high-resolution-melt analysis. (i) Box plots of normalised DNA quantities from Protoblock FFPE Escherichia (cyan) and NF Escherichia (orange). Significant shifts in the melting temperatures in 2 of the 3 sequences were observed as per Wilcoxon signed-rank test, with temperature shifts that were on average 0.1–0.5 °C apart from NF counterparts. (ii) Schematic of sequences used for HRM analysis: 3 DNA fragments with an average length of 100 bp were analysed. For each test and each sample type, n = 6. b Confirmation of sequence alteration by WGS. DNA from Protoblocks loaded with Escherichia and Staphylococcus and their NF paired reference was analysed by whole genome sequencing to determine chimeric reads and single-nucleotide polymorphisms (SNP) against the reference genome E. coli K12 MG1655 and S. aureus Newman. Here, the SNP are plotted on the x-axis and the rate of occurrence on the y-axis. Variant calling and level of coverage are measured using SAMTOOLS/BCFTOOLS. (i) Chimeric reads per layer of coverage. (ii) Distribution of SNPs found per bacterial strain