Two types of results are written to the Output Window: those containing
apparently consistent data about the relative orientations and positions
of contigs, and those that show inconsistencies in the data. The
inconsistencies will be due to misassembly or to misnaming of readings and
In the Output Window the program writes a line of information for each
template and a line of information for each reading from that template.
In order to restrict this information to fit on a standard 80 column
display a few abbreviations are used. An example for two consistent and
problematic template is shown below. Templates with possible problems are
separated from those without. The templates shown are sorted by problem;
consistent templates at the top followed by increasingly inconsistent
templates at the bottom.
Template zf18c8( 117), length 1400-2000(expected 1700)
Reading zf18a2.s1( +1F), pos 5620 +91, contig 46
Reading zf18c8.s1( -117F), pos 1084 +288, contig 127
Template zf98f4( 659), length 1400-2000(computed 7263)
Reading zf98f4.s1( -659F), pos 27 +238, contig 548
Reading zf98f4.r1( +800R), pos 5392 +211, contig 46
*** Possibly problematic templates listed below ***
Template zf24g6( 262), length 1400-2000(observed 1365)
D Reading zf24g6.r1( +808R), pos 463 +206, contig 46
D Reading zf24g6.s1( -262F), pos 1559 +268, contig 46
To describe the format of the template line we provide a detailed explanation
of the lines above for the last Template block.
"Template zf24g6( 262)"
This is template with name "zf24g6" and number 262.
These are the minimum and maximum lengths specified for this template.
This section has the general format of "comment(distance)", where "comment" is
one of the following.
The template has both forward and reverse readings within this contig. From
this information the actual size of the template can be seen. In the example
this is "1365".
The template length is estimated as the average of the specified minimum and
maximum size. This will be seen when the template does not span contigs and
does not have both forward and reverse primers visible.
The template has forward and reverse readings in different contigs. The length
is computed by butting the two contigs together, end to end, and finding the
resultant separation of the template ends. It is not possible to tell whether
the two contigs overlap, and if so by how much. Hence the "computed" lengths
should not be considered as absolute.
The first four characters may be either space or one of "?", "D", "P" or "S".
The meaning of each of these is as follows.
Absence of all of these characters means that the template is consistent.
No primer information is available for these readings.
The distance between forward and reverse primers (ie the template length) is
not as expected.
The primer information for readings on this template is inconsistent. An
example of this is where two forward readings exist, both using the universal
primer, and the readings are not in close proximity to each other.
The template strand information is inconsistent. This problem can be seen when
the forward and reverse readings are from the same strand, or two forward
readings are pointing in opposite directions.
The reading name
The reading number. The "+" or "-" character preceding the number represents
whether the reading has been complemented ("+" for original, "-" for
complemented). The letter following the number indicates the primer
information found for this reading. It may be one of:
Forward, universal primer
Forward, custom primer (eg a walk)
Reverse, universal primer
Reverse, custom primer
"pos 463 +206"
The position and the length of the reading within the contig. In this case the
reading starts at position 463 and extends for 206 bases. For a complemented
reading the position marks the 3' end of the reading. For both cases the
position can be considered as the 'left end' of the reading as displayed
within the contig.
The reading number of the left most reading within this contig.
In the above example the template has two readings. It can be seen that the
template starts at contig position 463 and finishes at position 1827. The
observed length is 1365, which is just below the expected minimum length of
1400. Hence the template is flagged as having an invalid distance. There are
no other inconsistencies for this template and so it is likely that the
only "problem" is that the experimental size selection process was not
as precise as was thought.
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Last generated on 22 October 2002.