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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 |
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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).
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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. |