Summary.csv File

The TruSeq Amplicon app produces an overview of statistics for each sample and the aggregate results in a comma-separated values (CSV) format: the *summary.csv. These files are located in the results folder for each sample and the aggregate results.

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.
Manifest	The manifest file used for analysis. This file specifies the targeted regions for the aligner and variant caller.
Reference genome	Reference genome selected.
Number of amplicon regions	Number of amplicon regions sequenced.
Total length of amplicon regions	Total length of sequenced bases in the target region.
Total PF reads	The number of reads passing filter for the sample.
Total aligned reads	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.
Percent aligned reads	Percentage of reads passing filter that aligned. Numbers are calculated per read, and over both reads.
Total PF bases	The number of bases passing filter for the sample.
Total aligned bases	Total number of bases present in the data set that aligned to the reference genome. Numbers are calculated per read, and over both reads.
Percent aligned bases	The percentage of bases that aligned to the reference genome. Numbers are calculated per read, and over both reads.
Percent Q30	The percentage of bases with a quality score of 30 or higher. Numbers are calculated per read.
Mismatch rate	The average percentage of mismatches across both reads 1 and 2 over all cycles. Numbers are calculated per read.
Amplicon mean coverage	The total number of aligned bases to the targeted region divided by the targeted region size.
SNVs, Insertions, Deletions	Total number of variants present in the data set that pass the quality filters.
SNVs, Insertions, Deletions (Percent found in dbSNP)	100*(Number of variants in dbSNP/Number of variants).
SNV 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 of purine and pyrimidine bases (for example, A to T).
SNVs, Insertions, Deletions Het/Hom ratio	Number of heterozygous variants/Number of homozygous variants.


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