The "Alignment Quality Overview", available via "ALIGNMENT QUALITY CONTROL" in the "RESULTS" menu option, displays the basic alignment quality results. Dependent on the actual sequencing type, the shown tables may differ.
Note that many of the statistics only use "QC-bases". QC-bases only include bases from aligned reads not marked as duplicates. Please refer to the workflow documentation for a detailed definition of QC-bases.
The following table explains the columns of the alignment overview table for WGS, WES, and WGBS data displayed in OTP:
| Value | Description |
|---|---|
| QC Status | Classification into QC "passed" or "failed". The actual classification also depends on the quality thresholds configured for your project. Please refer to "PROJECT" / "PROJECT CONFIG for details about QC threshold in your project. |
| Cov. w/o N | Ratio of mapped QC-bases and the genome size, only counting {A,C,G,T} bases |
| ChrX Cov. w/o N | The "Cov. w/o N" value only for the X-chromosome. |
| ChrY Cov. w/o N | The "Cov. w/o N" value only for the Y-chromosome. |
| Library Prep Kit | Name associated in OTP with a specific set of adapters and/or target region set (for WES data). |
| Mapped Reads % | #mappedReads / #allReads * 100; numbers according to samtools flagstat |
| Duplicates % | #duplicates / #allReads * 100; numbers according to samtools flagstat |
| Properly Paired % | #properlyPairedReads / #readsPairedInSequencing * 100; numbers according to samtools flagstat |
| Single % | #singletonReads / #allReads * 100; numbers according to samtools flagstat |
| Insert Size Median | Median of the insert size distribution |
| Diff Chrom % | #matesMappedToDifferentChromosomes / #allReads * 100 |
| Alignment | Alignment pipeline; currently only "bwa mem". |
For RNA-seq data quality values are shown that better account for the specific QC-requirements of this sequencing type. The workflow uses the RNA-SeQC tool, which is extensively documented here.
Here is a list of column names from the OTP overview table with explanations:
| Value | Description |
|---|---|
| QC Status | Classification into QC "passed" or "failed". The actual classification also depends on the quality thresholds configured for your project. Please refer to "PROJECT" / "PROJECT CONFIG for details about QC threshold in your project. |
| Total Read Counter | Total number of QC-passing reads according to samtools flagstat. |
| Duplicates % | Percentage of reads marked as duplicates according to samtools flagstat. |
| 3p Norm | according to RNA-SeQC. |
| 5p Norm | according to RNA-SeQC. |
| Chimeric Pairs | according to RNA-SeQC. |
| Duplication Rate of Mapped | according to RNA-SeQC. |
| End 1 Sense | according to RNA-SeQC. |
| End 2 Sense | according to RNA-SeQC. |
| Estimated Library Size | according to RNA-SeQC. |
| Exonic Rate | according to RNA-SeQC. |
| Expression Profiling Efficiency | according to RNA-SeQC. |
| Genes Detected | according to RNA-SeQC. |
| Intergenic Rate | according to RNA-SeQC. |
| Intragenic Rate | according to RNA-SeQC. |
| Mapped | according to RNA-SeQC. |
| Mapped Unique | according to RNA-SeQC. |
| Mapped Unique Rate of Total | according to RNA-SeQC. |
| Mapping Rate | according to RNA-SeQC. |
| Mean CV | according to RNA-SeQC. |
| Unique Rate of Mapped | according to RNA-SeQC. |
| rRNA Rate | according to RNA-SeQC. |
| Library Prep Kit | Name associated in OTP with a specific set of adapters. |