The Reading and Template Plot shows templates and readings. The following sections describe the display, its options, and the operations which it can be used to perform. It is invoked from the main gap4 View menu.
The Reading and Template Plot shows templates and readings. Colour is used to provide additional information. The reading colour is used to convey the primer information. The default colours are:
Colour is used to distinguish the number and the location of the readings derived from each template. Templates with readings derived from only one end are drawn in blue. Those with readings from both ends are pink when both ends are contained within the same contig. Those with readings from both ends are green when the readings are in different contigs and one of the contigs is not being plotted.
For each template gap4 stores an expected length, as a range between two values. From an assembly it is often possible to work out the actual length of a template based upon the positions within a contig of readings sequenced using the forward and reverse primers. The forward and reverse readings on a single template (called a read pair) are considered to be inconsistent if this observed distance is outside of the range of acceptable sizes and then the template is drawn in black. Alternatively it may be possible that both forward and reverse readings are assembled on the same strand (in which case both arrows will point in the same direction). This too is a problem and hence the templates are drawn in black.
If more than one contig is displayed then the distance between adjacent contigs is determined from any read pair information. If there are spanning templates between two adjacent contigs and the readings on that template are consistent, i.e. are in the correct orientation, the template is coloured yellow. Templates which span non-adjacent contigs in the display or contain inconsistent readings are coloured dark yellow.
A summary of the default template colours follows.
If more than one contig is displayed, the contigs are positioned in the same left to right order as the input contig list, (which need not necessarily be in the same order as the contig selector). Overlapping contigs are drawn as staggered lines. If the user selects the "Calculate contig positions" option from the menu the horizontal distance between adjacent contigs is determined from any available read pair information. Otherwise, or in the absence of any read pair information, the second contig is positioned immediately following the first contig, but will be drawn staggered in the vertical direction. If the readings on a template spanning two contigs are consistent, the distance between the contigs is determined using the template's mean length. If there are several templates spanning a pair of contigs an average distance is calculated and used as the final offset between the contigs. Templates which span non-adjacent contigs or contain inconsistent readings are not used in the calculation of the contig offsets. It is possible that data in the database is inconsistent to such an extent that, although spanning templates have consistent readings, the averaging can lead to a display which shows the templates to have inconsistent readings, eg the readings are pointing in opposite directions.
A summary of the templates and readings used to calculate the distance between two contigs is displayed in the output window. An example is given below:
============================================================ Wed 02 Apr 10:35:51 1997: template display ------------------------------------------------------------ Contig zf98g12.r1(651) and Contig zf23d2.s1(348) Template zf22h7( 376) length 1893 Reading zf22h7.r1( +10R), pos 6257 +208, contig 651 Reading zf22h7.s1( -376F), pos 145 +331, contig 348 Template zf49f5( 536) length 1510 Reading zf49f5.r1( +255R), pos 6562 +239, contig 651 Reading zf49f5.s1( -536F), pos 227 +135, contig 348 Gap between contigs = -11 Offset of contig 348 from the beginning = 7674
The contig names and numbers are given in the top line. Below this, the spanning template name, number and length is displayed. Below this the reading name, whether the reading has been complemented (+: original -: complemented), number, primer information, starting position, length and contig number. This is of similar format to that displayed by the read pairs output.See section Find Read Pairs. The average gap between the contigs is given and finally the distance in bases between the start of the second contig and the start of the left most contig in the display.