Adjacent to the reading name is a coloured block indicating the
reliability of the template.
- Red
-
Strand conflict (e.g. two forward readings are assembled on opposing strands)
- Blue
-
Position conflict (e.g. the start of this template can be derived at
multiple positions due to more than one universal primer sequence, but
at positions > 100 base pairs apart).
- Pink
-
One end is not present in this contig, but is in another contig.
- Light grey
-
One template end sequence is not present in this database (ie not a read-pair)
- Medium grey
-
The measured template size is too large or too small
- Dark grey
-
Multiple problems
These correspond to the (larger) set of single-letter codes that are
listed in the editor information line
The "go to" and "select all readings from this template" commands
(obtained by right clicking on the reading name) are particularly
useful when dealing with inconsistent templates.
The colour codes map to the (larger) set of single-letter identifiers
used in the information line
(see section The Editor Information Line).
The letter codes are:
- D
-
Distance (negative in size)
- d
-
Distance (too large/small)
- P
-
Primer position
- S
-
Strand
- E
-
Guessed start or end position of template
- I
-
Spans contigs and contig-end distance is large
- O
-
Spans contigs, but contig-end distance is small
- ok
-
No problems
- ?
-
Unknown problem
For templates with read-pairs spanning two contigs the distance from
the end of each contig (in the direction that the template 'reads' in)
is summed together to compute whether a contig join is viable. This in
turn yields the "O" and "I" codes.
Last generated on 25 November 2011.