Find Read Pairs Text Output

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 templates.

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 one 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

The Template Lines

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.

length 1400-2000

These are the minimum and maximum lengths specified for this template.

observed(1365)

This section has the general format of "comment(distance)", where "comment" is one of the following.

observed

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".

expected

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.

computed

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 Reading Lines

"?DPS"

The first four characters may be either space or one of "?", "D", "P" or "S". The meaning of each of these is as follows.

?

No primer information is available for these readings.

D

The distance between forward and reverse primers (ie the template length) is not as expected.

P

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.

S

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.

Absence of all of these characters means that the template is consistent.

"Reading zf24g6.r1"

The reading name

"( +808R)"

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:

?

Unknown

F

Forward, universal primer

f

Forward, custom primer (eg a walk)

R

Reverse, universal primer

r

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.

"contig 46"

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.