This section contains results from a software tool called MultiQC that calculates multiple quality control (QC) metrics associated with Illumina sequencing data (Code and documentation available at https://multiqc.info/). These metrics can be useful for diagnosing problems that occur during sequencing or library construction. Please note that Center staff review these metrics and will flag any concerns. For users interested in more detail, A full MultiQC report for your samples can be viewed by following the link below the plots: "view full MultiQC report (in new window)". In addition, we provide three of the most commonly viewed plots are shown here for convenience:
a. Per base N content. This plot shows the percentage of reads with a no-call base (“N”) at each position along the read length for each library. It is typical to see slightly elevated N content of ~0.5% at the beginning and end of the read. Other anomalies can indicate technical problems during the sequencing run.
b. Mean Quality Scores. This plot the average base call quality score (“phred” score) at each position along the read length for each library. It is typical to see slightly lower scores at the beginning and end of the read. Average scores below 30 can indicate technical problems during the sequencing run.
c. FastQC: Sequence Duplication Levels. This plot shows the percentage of sequences in the library that are present at different frequencies. This can provide an early indication of library complexity, but the post-alignment metrics described in sections 3a and 3b below are usually more informative.