Flags
The workbench's use of the alignment flags is shown in the following table and subsequent examples.
| Bit | SAM description | Usage in Workbench |
| 0x1 | template having multiple segments in sequencing | set if the segment is part of a pair |
| 0x2 | each segment properly aligned according to the aligner | set if the pair is not broken |
| 0x4 | segment unmapped | never set since the exporter does not export unmapped reads |
| 0x8 | next segment in the template unmapped | never set by the exporter. If a segment has an unmapped mate, the flag 0x1 is not set for the segment, i.e.is not output as part of a pair |
| 0x10 | SEQ being reverse complemented | set if and only if the segment was reverse complemented during mapping |
| 0x20 | SEQ of the next segment in the template being reversed | set if and only if the mate was reverse complemented during mapping |
| 0x40 | the first segment in the template | this mate is the first segment of the pair |
| 0x80 | the last segment in the template | this mate is the second segment of the pair |
| 0x100 | secondary alignment | never set by the exporter and ignored by the importer |
| 0x200 | not passing quality controls | never set by the exporter and ignored by the importer |
| 0x400 | PCR or optical duplicate | never set by the exporter and ignored by the importer |
Subsections