Aggregate Summary Report

The Aggregate Summary report is available if more than one sample pair was analyzed. The Aggregate Summary report aggregates all the individual Pairwise Analysis reports for the project into a single report. The information is shown is tables and in plots. For any plot in the report, you can place your cursor on a data point to open a tooltip that shows the name of the associated sample and the value for the report metric. The Aggregate Summary report page also has an option for downloading the Summary Report (Manifest Information, Sample Information, and Aggregate Summary Details) as a PDF.

Manifest Information

The manifest is the list of targeted regions that were analyzed.

note

The Manifest Information is a fixed parameter for Amplicon DS.

Amplicon Summary

 

• Read Level Statistics

The Percent Aligned Reads is plotted against each sample for each analyzed pair, resulting in a single plot with one data point per sample pair. The following metrics are detailed in a table above the plot:

Statistic Definition

Total Aligned Reads (R1/R2)

 The total number of reads passing filter present in the data set that aligned to the reference genome. Numbers are per read.
Percent Aligned Reads (R1/R2)

The percentage of reads passing filter that aligned to the reference genome.
Overall Percent Aligned Reads The percentage of reads passing filter that aligned to the reference genome across both reads (R1 and R2). The value is the average of the individual Percent Aligned Reads values.
• Base Level Statistics
The Percent Aligned Bases is plotted against each sample for each analyzed pair, resulting in a single plot with one data point per sample pair. The following metrics are detailed in a table above the plot:
Statistic Definition

Total Aligned Bases (R1/R2)

The total number of bases present in the data set that aligned to the reference genome. Numbers are per read.
Overall Total Aligned Bases The total number of bases present in the data set that aligned to the reference genome across both reads (R1 and R2). The value is the average of the individual Total Aligned Bases values.

Percent Aligned Bases (R1/R2)

The percentage of bases that aligned to the reference genome.

Numbers are per read.
Overall Percent Aligned Bases The percentage of bases that aligned to the reference genome across both reads (R1 and R2). The value is the average of the individual Percent Aligned Bases values.
Percent Q30 The percentage of bases with a quality score of 30 or higher.
Mismatch Rate The percentage mismatch to the reference genome averaged over cycle per read (R1 and R2).

Small Variants Summary

• SNVs

The total number of SNVs that passed the quality filters is plotted against each sample for each analyzed pair, resulting in a single plot with one data point per sample pair. The following metrics are detailed in a table above the plot:

 

Statistic Definition

SNVs

 The total number of variants present in the data set that passed the variant quality filters.

Percent Found in dbSNP

100*(Number of SNVs in dbSNP/Number of SNVs). The SNVs that were found in the dbSNP are annotated accordingly.

Ts/Tv Ratio

 Transition rate of SNVs that pass the quality filters divided by transversion rate of SNVs that pass the quality filters. Transitions are interchanges of purines (A, G) or of pyrimidines (C, T). Transversions are interchanges between purine and pyrimidine bases (for example, A to T).

SNV Het/Hom Ratio

 Number of heterozygous variants/Number of homozygous variants.
• Insertions

The total number of insertions that passed the quality filters is plotted against each sample for each analyzed pair, resulting in a single plot with one data point per sample pair. The following metrics are detailed in a table above the plot:

 

Statistic Definition

Insertions

 The total number of variants present in the data set that passed the variant quality filters.
Percent Found in dbSNP

100*(Number of SNVs in dbSNP/Number of SNVs). The SNVs that were found in the dbSNP are annotated accordingly.

Insertion Het/Hom Ratio

 Number of heterozygous variants/Number of homozygous variants.
• Deletions

The total number of deletions that passed the quality filters is plotted against each sample for each analyzed pair, resulting in a single plot with one data point per sample pair. The following metrics are detailed in a table above the plot:

 

Statistic Definition

Deletions

 The total number of variants present in the data set that passed the variant quality filters.
Percent Found in dbSNP

100*(Number of SNVs in dbSNP/Number of SNVs). The SNVs that were found in the dbSNP are annotated accordingly.

Deletions Het/Hom Ratio

 Number of heterozygous variants/Number of homozygous variants.

Coverage Summary

The Amplicon Mean Coverage Depth is plotted against each sample for each analyzed pair, resulting in a single plot with one data point per sample pair. The following metrics are detailed in a table above the plot:

Statistic Definition

Amplicon Mean Coverage Depth

 The total number of aligned bases to the targeted region divided by the targeted region size.
Uniformity of Coverage The percentage of amplicon regions with coverage values greater than the low coverage threshold, where the low coverage threshold is defined as (0.2 * Amplicon Mean coverage).

 

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