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2. GS Reference Mapper : 2.10 Using the Variants Tab : 2.10.1 The HC Diffs Sub-Tab
2.10.1
The HC Diffs Sub-Tab
Information about local differences between reads and the reference appear in a table on the HC Diffs sub-tab. Explanations for each of the columns in the table are found in the description of the 454AllDiffs.txt file, in Section 2.17.1.13. Right-clicking on a row opens a contextual menu from which one can access the alignment that underlies the variation. Pausing the mouse over a row displays a tooltip providing information about that variation.
The tab can be divided conceptually into four main functional sections (Figure 63):
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The leftmost columns (from Reference Accession Number to Total Depth) contain general information on the high confidence differences (HCDiffs) that were found in the computed data, between the reads and the reference sequences.
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The center columns (from Reference Amino Acids to Known SNP Info) show gene annotation or known SNP file information on the regions of the HCDiffs. For such information to be available, Genome Annotation and Known SNP databases must have been specified (either on the Parameters Tab or by using a Golden Path reference sequence).
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The columns from Percent Forward to Total Num Reverse Reads contain a detailed breakdown of the computation data shown on the left.
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The last column, Target Region Status, is filled if the project is run with a targeted region file, and indicates whether the HCDiff is in a targeted region or in an extended region. HCDiffs outside extended target regions are not reported in this table.
Figure 63: gsMapper Variants tab, HC Diffs sub-tab