The score to pass alignment is 30 by default, but may be changed in the settings menu. This score is essentially the Smith-Waterman score from BWA-MEM, which, for example, gives a +1 for each perfect match and a –1 for each mismatch in the read. For example, with the default score, there may be 30 perfectly matched bases, or 32 matches with 2 indels, or 33 matches and 3 indels, etc.
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