Enrichment Sequencing Report

The Isaac Enrichment app provides an aggregate summary PDF report for all samples combined on the Summary page.

This section contains a description of the report.

NOTE

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

Manifest Information

Provides the target manifest name, and the following metrics:

Statistic	Definition
Total length	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.

Sample Information

Defines the sample numbers and names in the report.

Enrichment Summary

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Read Level Enrichment

Statistic	Definition
Total Aligned Reads	The total number of reads passing filter present in the data set that aligned to the reference genome.
Targeted Aligned Reads	Number of reads that aligned to the target.
Read Enrichment	100*(Target aligned reads/Total aligned reads).
Padded Target Aligned Reads	Number of reads that aligned to the padded target.
Padded Read Enrichment	100*(Padded target aligned reads/Total aligned reads).

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Base Level Enrichment

Statistic	Definition
Total Aligned Bases	The total number of bases present in the data set that aligned to the reference genome.
Targeted Aligned Bases	Total aligned bases in the target region.
Base Enrichment	100*(Total Aligned Bases in Targeted Regions/Total Aligned Bases).
Padded Target aAigned Bases	Total aligned bases in the padded target region.
Padded Base Enrichment	100*(Total Aligned Bases in Padded Targeted Regions/Total Aligned Bases).

The Base Enrichment histogram graphs the total aligned bases, padded targeted aligned bases, and padded base enrichment by sample.

SNV Summary

Statistic	Definition
SNVs	Total number of Single Nucleotide Variants present in the data set passing the quality filters.
SNVs (Percent Found in dbSNP)	100*(Number of SNVs in dbSNP/Number of SNVs). The SNVs that were found in the dbSNP are annotated accordingly.
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).
SNV Het/Hom Ratio	Number of heterozygous SNVs/Number of homozygous SNVs.

The SNVs histogram graphs the number of SNVs passing by sample.

Indel Summary

Statistic	Definition
Indels	Total number of indels present in the data set passing the quality filters.
Indels (Percent Found in dbSNP)	100*(Number of Indels in dbSNP/Number of Indels).
Indel Het/Hom Ratio	Number of heterozygous indels/Number of homozygous indels.

The Indels histogram graphs the number of indels passing by sample.

Coverage Summary

Statistic	Definition
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.

In addition, the app provides two graphs:

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A Coverage Mean and Uniformity histogram that plots the mean region coverage depth and uniformity of coverage by sample.

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A Depth of Coverage in Targeted Regions histogram that plots the number of targeted sequences by the depth of coverage.

Statistic	Definition
Depth of Sequencing Coverage	The coverage depth of a position in the genome refers to the number of sequenced bases that align to that position.
Number of Targeted Bases Covered	Number of targeted bases that have at least the indicated depth of coverage.

Fragment Length Summary

Statistic	Definition
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.
Minimum	Minimum length of the sequenced fragment.
Maximum	Maximum length of the sequenced fragment.
Standard Deviation	Standard deviation of the sequenced fragment length.

The Fragment Length Medians histogram graphs the fragment length median by sample.

Duplicates Summary

Statistic	Definition
Percent Duplicate Paired Reads	Percentage of paired reads that have duplicates.

The Percent Duplicate Paired Reads histogram graphs the percent duplicate paired reads by sample.


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