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| What are the various Allignmet Report Descriptions? |
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Last Updated
11th of April, 2012
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The various calculations for the Alignment report are as follows:
- Observation 1 (name of first half of pair)
- Observation 2 (name of second half of pair)
- MeanInsertSize (average insert size calculated across paired reads)
- Total read # (total # of reads)
- Uniquely paired read # (reads that are both uniquely mapped and paired)
- Non-uniquely paired read # (reads that are not uniquely mapped but are paired)
- Uniquely mapped read #1 (reads that are uniquely mapped, but not paired, from file #1)
- Uniquely mapped read #2 (reads that are uniquely mapped, but not paired, from file #2)
- Non-uniquely mapped read #1 (reads that are non-uniquely mapped, but not paired, from file #1)
- Non-uniquely mapped read #2 (reads that are non-uniquely mapped, but not paired, from file #2)
- Unmapped read #1 (reads that are unmapped from file #1)
- Unmapped read #2 (reads that are unmapped from file #2)
- Uniquely paired read % (percentage of reads that are both uniquely mapped and paired)
- Non-uniquely paired read % (percentage of reads that are not uniquely mapped but are paired)
- Uniquely mapped read 1 % (percentage of reads that are uniquely mapped, but not paired, from file #1)
- Uniquely mapped read 2 % (percentage of reads that are uniquely mapped, but not paired, from file #2)
- Non-uniquely mapped read 1 % (percentage of reads that are non-uniquely mapped, but not paired, from file #1)
- Non-uniquely mapped read 2 % (percentage of reads that are non-uniquely mapped, but not paired, from file #2)
- Unmapped read 1 % (percentage of reads that are unmapped from file #1)
- Unmapped read 2 % (percentage of reads that are unmapped from file #2)
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