I've assessed multiple RNA-seq data sets from human, some FFPE, some mRNA-seq, some clinical, some from cell culture, which were library prepped and sequenced at different facilitiies.
I've found that every single sample has reads mapping to the ampicillin resistance gene. I've BLASTed the reads that have mapped and found that they map perfectly to that gene and do not map to the human genome. Is there any technical reason why this would occur? Is this a common spike-in like phiX?