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Template Status Codes

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.


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Last generated on 25 November 2011.