If Mycoplasma RNA is present in a sample used as input for QuantSeq library prep, the following can be observed in data analysis:
Reduced overall mapping rates and reduced unique mapping rates to the target genome. In the most severe of cases, only ~30% of the reads can be mapped uniquely.
When mapping the reads to Mycoplasma, uniquely mapped reads can be identified. It may be that different mycoplasma species could be involved so mapping to different species could be advised. To check sequences, use BLASTn.