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 30.5
The second mate of a non-broken paired read 0x1, 0x2, 0x10, 0x80 147 See Figure 30.6
A single, forward read (or paired read, where only one mate of the pair is mapped) No set bits 0 see Figure 30.7
A single, reversed read (or paired read, where only one mate of the pair is mapped) 0x10 16 See Figure 30.8
The first, forward segment from a broken pair with forward mate 0x1, 0x40 65 See Figure 30.9
The second, forward segment from broken pair with reversed mate 0x1, 0x20, 0x80 161 See Figure 30.10
The first, reversed segment from broken pair with forward mate 0x1, 0x10, 0x40 81 See Figure 30.11
The second, reversed segment from broken pair with reversed mate 0x1, 0x10, 0x20, 0x80 177 See Figure 30.12

Image flag35
Figure 41.1: The read is paired, both reads are mapped and the mate of this read is reversed

Image flag19
Figure 41.2: The read is paired, both mates are mapped, and this segment is reversed

Image flag0
Figure 41.3: A single, forward read, or a paired read where the mate is not mapped

Image flag16
Figure 41.4: The read is a single, reversed read, or a paired read where the mate is not mapped

Image flag1
Figure 41.5: These forward reads are paired. They map to the same place, so the pair is broken

Image flag1
Figure 41.6: Forward read that is part of a broken read where the mate is reversed

Image flag17
Figure 41.7: Reversed read that is part of a broken pair, where the mate is forward

Image flag49-1
Figure 41.8: Reversed read that is part of a broken pair, where the mate is also reversed.