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, 16:30, 30 September 2010
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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). |
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| '''What should the quality count as if the quality string is '*'?''' | | '''What should the quality count as if the quality string is '*'?''' |