Genome Browser BAM tracks may be configured in a variety of ways to
highlight different aspects of the displayed information.
The configuration options are described here and related to custom track
settings that can alter the default appearance of the custom track.
Click here for more information
on BAM custom track creation.
- Attempt to join paired end reads by name:
This checkbox appears only if pairEndsByName is included in the
track settings. When checked, SAM/BAM records with the same name will be
joined into pairs for display, with a line drawn between them.
- Minimum alignment quality:
Exclude alignments with quality less than the given number. The default is 0,
unless changed by the track setting minAliQual.
- Color track by bases:
By default, mismatching bases are highlighted in the display.
Change the selection to "item bases" to see all base values from
the query sequence, or "OFF" to ignore query sequence.
- Additional coloring modes:
Other aspects of the alignments can be displayed in color or grayscale.
The default mode is 'Color by strand' (bamColorMode=strand), unless
the bamColorMode track setting specifies gray, tag
- Color by strand:
alignments on the reverse strand are colored dark red, alignments on the
forward strand are colored dark blue.
items are shaded according to the chosen method:
alignment quality, base qualities, or unpaired ends.
Items' alignment qualities are shaded on a scale of 0 (lightest) to 99 (darkest).
Base qualities are shaded on a scale of 0 (lightest) to 40 (darkest).
When "unpaired ends" is selected, items that were paired in sequencing
but whose mate was not mapped are colored gray, while singletons and properly
paired items are black.
Alignment quality is the default (bamGrayMode=aliQual) unless
bamGrayMode track setting is baseQual or unpaired.
- Use R,G,B colors specified in user-defined tag:
SAM/BAM may include user-defined tags, whose names begin with X, Y or Z
and include one other letter or number. The user-defined tag named here
specifies red, green and blue (RGB) intensities as a zero-terminated string
(tag type Z) containing comma-separated triples
of numbers from 0-255. For example, if a SAM/BAM record includes the tag
YC:Z:255,0,0, then the item is colored red;
YC:Z:0,0,255 makes the item blue.
By default, the tag is "YC" unless changed using the track setting
- No additional coloring
- Display data as a density graph: This feature enables the BAM data to be
displayed as a bar graph where the height is proportional to the number of reads
mapped to each genomic position. Through dynamic calculation of items in
the current window, this feature plots a line similar to a wiggle graph that
can be customized with a number of graph-based configuration options such as drawing indicator lines,
smoothing plots, adjusting graph height and vertical range, and switching from bars
to points. Please note that the feature is best displayed with Display mode
set to full and that the default Data view scaling is
auto-Scale to data view.
Also, please note that when set to display as a density graph, other BAM
display options described on this page, such as coloring for strand, alignment
quality and base qualities, are not applied.
When you have finished making your configuration changes, click the
Submit button to return to the annotation track display