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. it 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. No reads with this flag set are imported39.1. |
| 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 |
Flag Examples
The following table illustrates some of the possible flags in the workbench.
| Description of the example | Bits | Flag | Illustration |
| The first mate of a non-broken paired read | 0x1, 0x2, 0x20, 0x40 | 99 | See Figure 36.2 |
| The second mate of a non-broken paired read | 0x1, 0x2, 0x10, 0x80 | 147 | See Figure 36.3 |
| A single, forward read (or paired read, where only one mate of the pair is mapped) | No set bits | 0 | see Figure 36.4 |
| A single, reversed read (or paired read, where only one mate of the pair is mapped) | 0x10 | 16 | See Figure 36.5 |
| The first, forward segment from a broken pair with forward mate | 0x1, 0x40 | 65 | See Figure 36.6 |
| The second, forward segment from broken pair with reversed mate | 0x1, 0x20, 0x80 | 161 | See Figure 36.7 |
| The first, reversed segment from broken pair with forward mate | 0x1, 0x10, 0x40 | 81 | See Figure 36.8 |
| The second, reversed segment from broken pair with reversed mate | 0x1, 0x10, 0x20, 0x80 | 177 | See Figure 36.9 |
Figure 39.1: The read is paired, both reads are mapped
and the mate of this read is reversed
Figure 39.2: The read is paired, both mates are mapped, and this segment is reversed
Figure 39.3: A single, forward read, or a
paired read where the mate is not mapped
Figure 39.4: The read is a single, reversed read, or a
paired read where the mate is not mapped
Figure 39.5: These forward reads are paired. They map to the
same place, so the pair is broken
Figure 39.6: Forward read that is part of a broken read
where the mate is reversed
Figure 39.7: Reversed read that is part of a broken
pair, where the mate is forward
Figure 39.8: Reversed read that is part of a broken
pair, where the mate is also reversed.
Footnotes
- ... imported39.1
- The representation of a particular read with more than one location in a mapping is not supported in the software and thus cannot be imported.