Analysis Output | Enrichment Summary Report

Enrichment Summary Report

The BWA Enrichment App produces an enrichment summary report and the aggregate results in a comma-separated values (CSV) format: *.summary.csv. These files are located in the analysis results folder for each sample and the aggregate results.

NOTE

PCR duplicate reads are not removed from statistics. Results are not directly comparable to Picard HsMetrics.

Statistic	Definition
Sample ID	IDs of samples reported on in the file.
Sample Name	Names of samples reported on in the file.
Run Folder	Run folders for samples reported on in the file.
Reference Genome	Reference genome selected.
Target Manifest	The target manifest file used for analysis. This file specifies the targeted regions for the aligner and variant caller.
Total Length of Targeted Reference	The total length of the sequenced bases in the target region.
Padding Size	The length of sequence immediately upstream and downstream of the enrichment targets that is included for a padded target.
Total PF Reads	The number of reads passing filter for the sample.
Total Aligned Reads	The total number of reads passing filter present in the data set that aligned to the reference genome.
Percent Aligned Reads	The percentage of reads passing filter that aligned to the reference genome.
Percent Duplicate Paired Reads	Percentage of paired reads that have duplicates.
Targeted Aligned Reads	Number of reads that aligned to the target.
Padded Target Aligned Reads	Number of reads that aligned to the padded target.
Read Enrichment	100*(Target aligned reads/Total aligned reads).
Padded Read Enrichment	100*(Padded target aligned reads/Total aligned reads).
Total PF Bases	The number of bases passing filter for the sample.
Percent Q30	The percentage of bases with a quality score of 30 or higher.
Percent Q30 Aligned	Percent of bases with a quality score of 30 or higher that aligned to the reference genome.
Total Aligned bases	The total number of bases present in the data set that aligned to the reference genome.
Percent Aligned bases	Percent aligned bases in the target region.
Targeted Aligned bases	Total aligned bases in the target region.
Padded Target Aligned bases	Total aligned bases in the padded target region.
Base Enrichment	100*(Total Aligned Bases in Targeted Regions/Total Aligned Bases).
Padded Base Enrichment	100*(Total Aligned Bases in Padded Targeted Regions/Total Aligned Bases).
Mean Region Coverage Depth	The total number of aligned bases to the targeted region divided by the targeted region size.
Uniformity of Coverage (Pct > 0.2*mean):	The percentage of targeted base positions in which the read depth is greater than 0.2 times the mean region target coverage depth.
Target Coverage at 1X	Percentage targets with coverage greater than 1X.
Target Coverage at 10X	Percentage targets with coverage greater than 10X.
Target Coverage at 20X	Percentage targets with coverage greater than 20X.
Target Coverage at 50X	Percentage targets with coverage greater than 50X.
Fragment Length Median	Median length of the sequenced fragment. The fragment length is calculated based on the locations at which a read pair aligns to the reference. The read mapping information is parsed from the BAM files.
Fragment Length Min	Minimum length of the sequenced fragment.
Fragment Length Max	Maximum length of the sequenced fragment.
Fragment Length SD	Standard deviation of the sequenced fragment length.
SNVs, Indels, Insertions, Deletions	Total number of variants present in the data set that pass the quality filters.
SNVs (All), Indels (All), Insertions (All), Deletions (All)	Total number of predicted variants in the data set.
SNVs, Indels, Insertions, Deletions (Percent Found in dbSNP)	100*(Number of variants in dbSNP/Number of variants).
SNV Ts/Tv ratio	The number of Transition SNVs that pass the quality filters divided by the number of Transversion SNVs that pass the quality filters. Transitions are interchanges of purines (A, G) or of pyrimidines (C, T). Transversions are interchanges of purine and pyrimidine bases (for example, A to T).
SNVs, Indels, Insertions, Deletions Het/Hom ratio	Number of heterozygous variants/Number of homozygous variants.
SNVs, Insertions, Deletions in Genes	The number of variants that fall into a gene.
SNVs, Insertions, Deletions in Exons	The number of variants that fall into an exon.
SNVs, Insertions, Deletions in Coding Regions	The number of variants that fall into a coding region.
SNVs, Insertions, Deletions in Mature miRNA	The number of variants that fall into a mature microRNA.
SNVs, Insertions, Deletions in UTR Region	The number of variants that fall into an untranslated region (UTR).
SNVs, Insertions, Deletions in Splice Site Region	The number of variants that fall into a splice site region.
Stop Gained SNVs, Insertions, Deletions	The number of variants that cause an additional stop codon.
Stop Lost SNVs, Insertions, Deletions	The number of variants that cause the loss of a stop codon.
Frameshift Insertions, Deletions	The number of variants that cause a frameshift.
Non-synonymous SNVs, Insertions, Deletions	The number of variants that cause an amino acid change in a coding region.
Synonymous SNVs	The number of variants that are within a coding region, but do not cause an amino acid change.