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Table 1 Obtained and validated SNPs per parameter set. Of the six tested parameter combinations, the lowest false positive rate was retrieved with the default values: 15 Minimum coverage and 70 Minimum average quality

From: 4Pipe4 – A 454 data analysis pipeline for SNP detection in datasets with no reference sequence or strain information

  Parameters used (Min. Average Quality)
10|60 10|70 15|60 15|70 (Default) 10|75 20|70
Total SNPs retrieved 234 169 155 114 107 89
Confirmed SNPs 97 86 88 82 69 57
False Positive rate (%) 58.55 49.11 43.23 28.07 35.51 35.96