Flags

The use of alignment flags by the CLC Genomics Workbench is shown in the following table and subsequent examples.

Bit SAM description Usage
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 imported.
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 CLC Genomics Workbench.

Description of the example Bits Flag Illustration
The first mate of a non-broken paired read 0x1, 0x2, 0x20, 0x40 99 Figure 38.2
The second mate of a non-broken paired read 0x1, 0x2, 0x10, 0x80 147 Figure 38.3
A single, forward read (or paired read, where only one mate of the pair is mapped) No set bits 0 Figure 38.4
A single, reversed read (or paired read, where only one mate of the pair is mapped) 0x10 16 Figure 38.5
The first, forward segment from a broken pair with forward mate 0x1, 0x40 65 Figure 38.6
The second, forward segment from broken pair with reversed mate 0x1, 0x20, 0x80 161 Figure 38.7
The first, reversed segment from broken pair with forward mate 0x1, 0x10, 0x40 81 Figure 38.8
The second, reversed segment from broken pair with reversed mate 0x1, 0x10, 0x20, 0x80 177 Figure 38.9

Image flag35
Figure 38.2: The read is paired, both reads are mapped and the mate of this read is reversed

Image flag19
Figure 38.3: The read is paired, both mates are mapped, and this segment is reversed

Image flag0
Figure 38.4: A single, forward read, or a paired read where the mate is not mapped

Image flag16
Figure 38.5: The read is a single, reversed read, or a paired read where the mate is not mapped

Image flag1
Figure 38.6: These forward reads are paired. They map to the same place, so the pair is broken

Image flag1
Figure 38.7: Forward read that is part of a broken read where the mate is reversed

Image flag17
Figure 38.8: Reversed read that is part of a broken pair, where the mate is forward

Image flag49-1
Figure 38.9: Reversed read that is part of a broken pair, where the mate is also reversed.