Viewing Reads Mapped to the Reference with the Alignment Results Tab

2.12	Viewing Reads Mapped to the Reference with the Alignment Results Tab

Click on the Alignment results tab to view the alignment data from the mapping computation (Figure 67). This tab shows the multiple alignments underlying the mapping of the reads to the reference.

Figure 67: gsMapper Alignment results tab

•	The left-hand panel contains a sortable table of References.

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When an entry in that table is selected, the corresponding alignment results are displayed in the main window. The table columns include the accno, number of bases, and the number of contigs in each reference. Sorting by number of contigs (contiguous portions of the reference covered by at least a minimum number of reads) is helpful when the reads are expected to map to only a few of many reference sequences.

•	The first row of the multiple alignment in the main window contains the reference sequence for the selected multiple alignment, gapped for insertions in the aligned reads.

•	The successive lines display the individually aligned reads, gapped and showing bases that diverge from the consensus as red dashes on yellow background.

•	Chimeric reads may participate in more than one multiple alignment. In order to distinguish the chimerically mapped segments of a read, a segment number between square brackets (e.g. [1], [2], etc) is appended to the accession number of the read in the alignment view.

•	Scroll bars allow you to navigate the alignment manually:

•	Clicking on the arrowheads on either side of a scroll bar scrolls the alignment by one base (horizontal) or one read (vertical) in the direction of the arrowhead

•	Clicking on the light-colored area on either side of the horizontal scroll bar “handle” scrolls the alignment by 40 bases is the corresponding direction

•	Clicking and dragging the “handle” of a scroll bar allows you to move larger distances rapidly

•	For easy viewing, when a base position is selected, the base position column is highlighted so that individual variations may be easily identified.

•	Right-clicking on a GS read will produce a “Get flowgram for … at selected position” menu item which, if selected, will activate the Flowgrams tab and display the flowgram for the read; centered on the flow corresponding to the base on which the user clicked to activate the option.

This capability is not active for FASTA/FASTQ reads or the contig/consensus sequences themselves, for which no flowgrams are available.

•	Above the Main window, the selected contig information is displayed. Below this is the base view information reporting the selected base and the left and right view positions in the current window.

•	To the right of these information fields are tools for viewing and data capture of the main window alignments:

◦	Go To: A data entry field and a Go To button allow you to navigate directly to a position of interest: enter a number not larger than the length of the selected contig in the data entry field, and click the Go To button.

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The zoom-slider tool allows for more or fewer bases to be viewed at a time in the main window. If the slider is set to all the way zoom out (-) then the individual bases are grayed out but the shape of the read alignment is still shown along with the positions of the high quality differences highlighted in yellow. (Figure 68).

◦	A ‘zoom to selected’ button can be used to zoom in, centering on the selected base. If no base is selected, it will use the base in the center of the current view as a default.

◦	Camera icon: saves an image of the part of the multi-alignment table currently visible on screen, to a file in .png format.

•	The Alignment Results tab also features a “Mouse Tracker” area, in the left panel, below the list of reference sequences. If you pause the mouse pointer over a base in the multi-alignment, the following information is provided about that base:

◦	Base: the position of that base relative to the selected reference sequence; gaps in the reference sequence are displayed as the following base of the reference

◦	Read: the name of the read or contig to which this base belongs

◦	Val: the “value” of the base under the mouse pointer, in that read, i.e. A, G, T, or C.

Figure 68: gsMapper Zoom Slider - all the way out.

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Finally, a drop down menu of Positions of Interest exists near the upper right corner of the gsMapper Alignment results tab (Figure 69). This is populated with contig positions for a chosen reference or the position(s) from the HCDiff and HC Structural Variants tables. The Positions of interest list allows the user to “go to” base positions without having to type in the value and using the go to button. There are next and previous buttons to move through the list.

Figure 69: gsMapper Alignment Results Tab