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Enrichment Summary Report

The Enrichment App produces an enrichment summary report in a comma-separated values (CSV) format (*.summary.csv). The file is located in the analysis results folder under Output Files.

NOTE

Some metrics are only reported if they are requested in the sample sheet. For example, the summary report can include different metrics for samples that are flagged as duplicates or not duplicates.

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

The selected reference genome.

Paired End

Boolean identifies whether the sample is paired-end or single-end.

Metrics Version

The PUMA metrics version.

Percent Callability

The percent of non-N reference positions in targeted regions with a passing genotype call.

Percent Autosome Callability

The percent of non-N reference positions in targeted regions in autosomal chromosomes with a passing genotype call.

Metrics Deliverable

The type of metrics in the summary file.

Enrichment Summary Format Version

The version of metrics in the summary file.

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.

Number of Targeted Regions

The number of target regions in the manifest file.

Padding Size

The length of sequence immediately upstream and downstream of the enrichment targets that is included for a padded target.

Target Unique Aligned Reads

The number of reads that align to the target and are not flagged as duplicates.

The statistic does not include the following reads:

• non-PF
• Unmapped
• Flagged as duplicate
• Secondary alignment

Padded Target Unique Aligned Reads

The number of reads that align to the padded target and are not flagged as duplicates.

Unique Read Enrichment

100* (Targeted unique aligned reads/Unique aligned reads)

Padded Unique Read Enrichment

100* (Padded targeted unique aligned reads/Unique aligned reads)

Total PF Reads

The total number of pass-filter reads for the sample.

Total PF Read 1

The total number of pass-filter reads for Read 1.

Total PF Read 2

The total number of pass-filter reads for Read 2.

Unique PF Reads

The total number of pass-filter reads that are aligned and are not flagged as duplicates.

Total Aligned Reads

The total number of pass-filter reads in the data set that aligned to the reference genome.

Unique Aligned Reads

The number of pass-filter reads that are aligned and are not flagged as duplicates.

Total Duplicate Aligned Reads

The number of pass-filter reads that are aligned and are flagged as duplicates.

Percent Duplicate Aligned Reads

The percentage of paired-end reads that are flagged as duplicates.

Total Aligned Read 1

The total number of reads passing filter that are aligned for Read 1.

Total Aligned Read 2

The total number of pass-filter reads that are aligned for Read 2.

Percent Aligned Reads

The percentage of pass-filter reads that are aligned to the reference genome.

Percent Unique Aligned Reads

The percentage of pass-filter reads that are aligned to the reference genome and are not flagged as duplicates.

Percent Aligned Read 1

The percentage of pass-filter reads that are aligned for Read 1.

Percent Aligned Read 2

The percentage of pass-filter reads that are aligned for Read 2.

Percent Duplicate Proper Read Pairs

The percentage of duplicate reads that are paired properly, where the reads are aligned inwards [--> < --] within a reasonable distance.

Targeted Unique Aligned Bases

The total aligned bases in the target regions of reads that are not flagged as duplicates.

Padded Target Unique Aligned Bases

The total aligned bases in the padded target regions of reads that are not flagged as duplicates.

Unique Base Enrichment

100* (Targeted unique aligned bases/Unique aligned bases).

 

Padded Unique Base Enrichment

100* (Padded target unique aligned bases/Unique aligned bases).

Targeted Unique Overlapping Bases

The number of unique PF bases where the base call corresponds to a fragment position that is in both Read 1 and Read 2 of a paired-end read.

Percent Targeted Unique Overlapping Bases

The percent of unique PF bases where the base call corresponds to a fragment position that is in both Read 1 and Read 2 of a paired-end read.

Total PF Bases

The total number of pass-filter read bases for the sample.

Unique PF Bases

The number of unique pass-filter read bases for the sample

Total PF Bases Read 1

The number of Read 1 pass-filter read bases for the sample.

Total PF Bases Read 2

The number of Read 2 pass-filter read bases for the sample.

Percent Q30 Bases

The percentage of bases with a 30 or above quality score.

Percent Q30 bases read 1

The percentage of Read 1 bases with a 30 or above quality score.

Percent Q30 bases read 2

The percentage of Read 2 bases with a 30 or above quality score.

Total Aligned Bases

The total aligned bases that includes reads flagged as duplicates.

Unique Aligned Bases

The total aligned bases that includes reads not flagged as duplicates.

Total Aligned Bases Read 1

The total aligned Read 1 bases that includes reads flagged as duplicates

Total Aligned Bases Read 2

The total aligned Read 2 bases that includes reads flagged as duplicates.

Percent Aligned Bases

100* (Total aligned bases/Total PF bases)

Percent Unique Aligned Bases

100* (Unique aligned bases / Unique PF bases)

Percent Aligned Bases Read 1

100* (Total aligned bases Read 1/Total PF bases Read 1)

Percent Aligned Bases Read 2

100* (Total aligned bases Read 2/Total PF bases Read 2)

Percent Mismatches

The percentage of unique aligned bases where the read base is different than the reference base.

Percent Mismatches Read 1

The percentage of unique aligned Read 1 bases where the Read 1 base is different than the reference base.

Percent Mismatches Read 2

The percentage of unique aligned Read 2 bases where the Read 2 base is different than the reference base.

Mean Target Coverage Depth

The total number of targeted bases divided by the targeted region size.

Number of Targeted Regions Covered End-to-End

The number of regions that are covered end-to-end with at least 1X coverage across all non-N reference positions.

Percent of Targeted Regions Covered End-to-End

The percentage of regions that are covered end-to-end with at least 1X coverage across all non-N reference positions.

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 of at least 1X.

Target Coverage at 10X

Percentage targets with coverage of at least 10X.

Target Coverage at 20X

Percentage targets with coverage of at least 20X.

Target Coverage at 50X

Percentage targets with coverage of at least 50X.

Fragment Length Median

The 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, Indels, Insertions, 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.

Nonsynonymous 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.

SV Insertions, Deletions, Tandem Duplications, Inversions, CNVs (All)

The number of structural variants in the data set.

SV Insertions, Deletions, Tandem Duplications, Inversions, CNVs

The number of structural variants in the data set that pass quality filters.

SV Insertions, Deletions, Tandem Duplications, Inversions, CNVs in genes

The number of structural variants that fall into a gene and pass quality filters.

SV Percent Insertions, Deletions, Tandem Duplications, Inversions, CNVs in genes

The percentage of structural variants that fall into a gene and pass quality filters.