Figure 5
Statistical evaluation and definition of plasmid contamination. Statistical evaluation and definition of plasmid contamination. Plasmid sequences not fulfilling the criteria mentioned are designated “artificial fragmented plasmids” The complete definition for an artificial fragmented plasmid is as following: “May contain several artificial sequences similar to a complete vector but is missing one criteria which can be: ori (O), selection marker (SM), promoter region with insert (I) regardless length and is not naturally occurring”. Due to the nature of fragmented plasmids, they may have either one or two features and are further characterized by them (e.g. ori with selection marker = O + SM). Sequences containing neither an ori, selection marker or insert but contained any other plasmid feature (e.g. histidine-tags) were termed very short fragments (VSF). A total of 80 plasmid sequences were found, representing 1.61% of all contigs. The total plasmid contamination varied from 0.16% in our control group up to 20.83% in a patient sample UJ. UK: Urine Volunteer K, UJ: Urine Volunteer J; UP: Urine Volunteer P; UN: Urine Volunteer N, RK: Nasopharyngeal Lavage Volunteer K, RJ: Nasopharyngeal Lavage Volunteer J, RP: Nasopharyngeal Lavage Volunteer P, RN: Nasopharyngeal Lavage Volunteer N, C03: Our Non-Template Control, R03: Technical Replicate Nasopharyngeal Lavage, U03: Technical Replicate Urine, Und: Undetermined Sequences.
