> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/dragen-5-base/additional-information/key-output-files-and-metrics/dragen-germline-with-no-variant-calling.md). # DRAGEN Germline with No Variant Calling ### Primary Annotation Files * bam​ * control.CX\_report.txt.gz​ * CX\_report.txt.gz ### Primary Metrics Files * fastqc\_metrics.csv​ * fragment\_length\_hist.csv​ * lambda\_unmethylated\_control.control.M-bias.txt​ * puc19\_methylated\_control.control.M-bias.txt​ * M-bias.txt​ * mapping\_metrics.csv​ * methyl\_metrics.csv​ * wgs\_contig\_mean\_cov.csv​ * wgs\_coverage\_metrics.csv​ * wgs\_overall\_mean\_cov.csv ### Mapping / Alignment Metrics The following can be extracted from \*mapping\_metrics.csv files: * Total reads​ * Total bases​ * Mapped reads percentage​ * Paired reads mapped to different chromosomes (MAPQ>=10) percentage​ * Mismatched bases R1 (excl. indels) percentage​ * Mismatched bases R1 (excl. indels) percentage​ * Q30 bases percentage​ * Not properly paired reads (discordant) percentage​ * Percentage of duplicate marked reads​ * Percentage of reads with MAPQ > 40​ * Soft-clipped bases R1​ * Soft-clipped bases R2 ### Coverage Metrics The following can be extracted from \*wgs\_coverage\_metrics.csv files: * Uniformity of coverage, percent of bases with coverage > 0.2 \* mean coverage​ * PCT of genome with coverage \[0x: 1x)​ * Average autosomal coverage over genome ### Methylation Calling Metrics The following can be extracted from \*methyl\_metrics.csv files: * % of Cs methylated in CpG context (tag in csv file: mCpGPer)​ * % of Cs methylated in CHG context (tag in csv file: mCHGPer)​ * % of Cs methylated in CHH context (tag in csv file: mCHHPer)​ * % of Cs methylated in unknown context (tag in csv file: mCunkPer)​ * The same 4 %C methylation metrics will be reported for the lambda and puc19 control genomes ### M-bias Metrics The following can be extracted from \*M-bias.txt files: * Counts of methylated and unmethylated Cs * % methylation and coverage for each position in read1 and read2 for CpG, CHG, and CHH contexts --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter: ``` GET https://help.connected.illumina.com/dragen-5-base/additional-information/key-output-files-and-metrics/dragen-germline-with-no-variant-calling.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.