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Summary File
The Amplicon DS App produces an Amplicon DS Summary Report for each sample and the aggregate results in a comma-separated values (CSV) format: *.summary.csv. These files are located in the results folder for each sample.
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Statistic |
Definition |
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Sample ID |
IDs of samples reported in the file. |
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Sample Name |
Names of samples reported in the file. |
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Run Folder |
Run folders for samples reported in the file. |
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Manifest |
The manifest file used for analysis. This file specifies the targeted regions for the aligner and variant caller. |
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Reference genome |
Reference genome selected. |
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Number of amplicons |
The number of amplicon regions sequenced. |
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Total length of amplicons |
The total length of the sequenced bases in the target region. |
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Total PF reads |
The number of reads passing filter for the sample. |
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Total aligned reads |
The total number of reads passing filter present in the data set that aligned to the reference genome. Numbers are calculated per read, and over both reads. |
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Percent aligned reads |
The percentage of reads passing filter that aligned to the reference genome. Numbers are calculated per read, and over both reads. |
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Total PF bases |
The number of bases passing filter for the sample. |
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Total aligned bases |
The total number of bases present in the data set that aligned to the reference genome. Numbers are calculated per read, and over both reads. |
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Percent aligned bases |
The percentage of bases that aligned to the reference genome. Numbers are calculated per read, and over both reads. |
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Percent Q30 |
The percentage of bases with a quality score of 30 or higher. Numbers are calculated per read. |
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Mismatch rate |
The average percentage of mismatches across both reads 1 and 2 over all cycles. Numbers are calculated per read. |
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Amplicon mean coverage |
The total number of aligned bases to the targeted region divided by the targeted region size. |
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Uniformity of Coverage |
The percentage of amplicon regions with coverage values of less than the low coverage threshold (0.2 * amplicon mean coverage). |
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SNVs, Insertions, Deletions |
Total number of variants present in the data set that pass the quality filters. |
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SNVs, Insertions, Deletions (Percent found in dbSNP) |
100*(Number of variants in dbSNP/Number of variants). |
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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). |
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SNVs, Insertions, Deletions Het/Hom ratio |
Number of heterozygous variants/Number of homozygous variants. |