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With the contamination flag, the assumption is that if a pest is present at high titer in a given sample and detection of reads matching to this pathogen in other samples occur at a significantly lower abundance, there is a risk that this lower signal is due to contamination (e.g. index hopping from high-titer sample). We first calculate the maximum FPKM value recorded for each virus and viroid identified on a run. If for a given virus, the FPKM value reported for a sample represented less than a percentage of this maximum FPKM value, it is then flagged as a contamination event. We apply 0.a 1% threshold value as default. This is just indicative and method cannot discriminate between false positives and viruses present at very low titer in a plant. It is then recommended to compare the sequences obtained, check the SNPs and validate through independent method.
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