This report provides an overview over general quality control measures of the sample and provides the summarized data as downloadable tables. For detailed information about the methods please consult the documentation.
Here, the information about read coverage of the reference genome as well as coverage of the mutation locations that were provided are listed. From those values, the overall quality of the sample can be assessed and whether or not its analysis results should and will be used for further trend-analysis and visualization.
In order to assess variant calling based on mutations of interest it is crucial that its genome locations are covered by read alignment. The table below shows the proportion of covered mutation locations, how many mutations are tracked in total, how many of their locations are covered and which locations have no read coverage at all.
This table shows the total number of raw reads, number of aligned reads, the mean coverage depth and percentage of the reference genome covered by pre-processed reads.
To improve alignment rates and mutation calling the pipeline contains trimming steps for primer, read-quality and adapter trimming. Parameter for read processing can be provided by the pipeline’s settings file. For detailed method information please consult the documentation.
In order to be able to assess and compare the read quality after each step multiple quality reports are generated which are presented below in a summarized format:
Download: MultiQC report of raw and processed data
To improve alignment rates and mutation calling proper trimming of reads should be considered e.g. based on the provided fastqc-reports. Read preprocessing is performed by Prinseq.
This sample was processed with these settings:
trim length cutoff prinseq | 0.2 |
Coverage statistics:
Download Coverage_stats.csv