You may view the Coverage Report for the currently selected contig or contig scaffold by selecting Contig > Coverage Report. This report summarizes coverage for the currently selected contig(s) in relation to the specified Strategy Viewing & Coverage parameters.
Note 1: The Coverage Report is not available for certain project types, including those assemblies without an associated capture region .bed file. For exome capture projects, view the Coverage of Target Regions report instead. For transcriptome assembles, view the Feature Table.
Note 2: For very large assemblies, the Coverage Report may be disabled by default. To enable the report, select a contig, then press and hold down the Alt key (Win) or Option key (Mac) while selecting Contig > Coverage Report. Note that the report may take much longer than usual to open.
There are two tabs available in the Coverage Report: All Coverage lists information for each distinct region of coverage in the selected contig(s); Below Coverage list information for only the areas of coverage that fall below the specified coverage threshold.
The following columns are displayed on each tab:
•Contig ID - The name of the contig.
•Type - The type of coverage for the particular region.
•Feature - If a feature on the reference sequence intersects the area of coverage, the feature name will be listed in this column.
Note: When a Coverage Report is created from features, the features are used to confine the coverage analysis to the areas that have features. In this case, the Feature column shows which feature was used to constrain the analysis area.
•Location - The range of sequence corresponding to the region of coverage.
•Length - The length of the range of sequence corresponding to the region of coverage.
•Depth - The minimum depth of coverage in the specified region. Note that adjacent areas with identical types of coverage will be combined.
•SNP Count – The number of variants in the region.
Right-click in the report to access context menu shortcuts to main menu commands.
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Command |
Shortcut to: |
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Undo |
Edit > Undo |
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Cut |
Edit > Cut |
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Copy |
Edit > Copy |
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Paste |
Edit > Paste |
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Clear |
Edit > Clear |
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Select All |
Edit > Select All |
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Show/Hide Column |
View > Show/Hide Column |
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Sort |
Contig > Sort |
Note: When working with an .sqd project, you must calculate variants using the Variant > Variant Report command before the SNP Count column will be displayed. This step is not necessary for BAM-based projects.