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:If either the reference or the read are 'N' or 'n', it is NOT a match or mismatch.
:If either the reference or the read are 'N' or 'n', it is NOT a match or mismatch.
:It is a match if the reference and the read have the same base (both A/a, both C/c, both G/g, or both T/t). If they are different, non-'N', bases it is a mismatch.
:It is a match if the reference and the read have the same base (both A/a, both C/c, both G/g, or both T/t). If they are different, non-'N', bases it is a mismatch.
'''What type of clip is used?'''
:When a read is clipped due to exceeding the mismatch threshold, a softclip is used (Cigar S).
'''What should the quality count as if the quality string is '*'?'''
'''What should the quality count as if the quality string is '*'?'''
