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In addition, the Post-alignment QA/QC report for single-end reads (Figure 1) contains the Unique column. This refers to the fraction of uniquely aligned reads.
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SubtitleText | Post-alignment QA/QC output table for single-end sequencing |
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AnchorName | result-table |
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On the other hand, the Post-alignment QA/QC report for paired-end reads (Figure 2) contains these columns:
- Unique singleton
- fraction of alignments corresponding to the reads where only one of the paired reads can be uniquely aligned
- Unique paired
- fraction of alignments corresponding to the reads where both of the paired reads can be uniquely aligned
- Non-unique singleton
- fraction of singletons that align to multiple locations
- Non-unique paired
- fraction of paired reads that align to multiple locations
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SubtitleText | Post-alignment QA/QC output table for paired-end sequencing |
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AnchorName | result-table-paired |
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In addition to the summary table, several graphs are plotted to give a comparison across multiple samples in the project. Those graphs are Alignment breakdown, Coverage, Average base quality per position, Average base quality score per read, and Average alignments per read. Two of those (Average base quality plots) have already been described.
The alignment breakdown chart (Figure 3) presents each sample as a column, and has two vertical axes (i.e. Alignment percent and Total reads). The percentage of reads with different alignment outcomes (Unique paired, Unique singleton, Non-unique, Unaligned) is represented by the left-side y-axis and visualized by stacked columns. The total number of reads in each sample is given using the black line and shown on the right-side y-axis.
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SubtitleText | Alignment breakdown plot. Each sample is a column. Fraction of reads with respect to their alignment status is given on the left-side y-axis and colour coded. Total number of reads is depicted by the black line and can be red on the right-side y-axis |
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AnchorName | breakdown-plot |
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The Coverage plot (Figure 4) shows the Average read depth (in covered regions) for each sample using columns and can be red off the left-hand y-axis. On the same plot, the percentage of covered genome bases (Genome coverage) in each sample is represented by the black line and quantified by the right-hand y-axis.
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SubtitleText | Coverage plot. Average read depth (times, in covered regions) is shown by columns and quantified on the left y-axis. Genome coverage (%) is shown by the black line and quantified on the right y-axis |
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AnchorName | coverage-plot |
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The last graph is Average alignments per read (Figure 5) and shows the average number of alignments for each read, with samples as columns. For single-end data, the expected average alignments per read is one, while for paired-end data, the expected average alignments per read is two.
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SubtitleText | Average alignments per read. Each sample is a column, average number of alignments per read is on the y-axis |
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AnchorName | avg-alignments |
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