Analysis Output | Output Files | Summary File

Summary File

The TruSeq Amplicon App produces an overview of statistics 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 and the aggregate results.

Statistic	Definition
Sample ID	IDs of samples reported in the file.
Sample Name	Names of samples reported in the file.
Run Folder	Run folders for samples reported in the file.
Reference genome	Reference genome selected.
Manifest	The manifest file used for analysis. This file specifies the targeted regions for the aligner and variant caller.
Number of amplicon regions	The number of amplicon regions that were sequenced.
Total length of amplicon regions	The total length of the sequenced bases in the targeted region.
Total PF reads	The number of reads passing filter for the sample.
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.
Percent aligned reads	The percentage of reads passing filter that aligned to the reference genome. Numbers are calculated per read, and over both reads.
Total probe bases	Total number of bases that aligned to the probe sequences (ULSO and DLSO) and are soft-clipped in the BAM files. Numbers are calculated per read, and over both reads.
Total aligned non-probe bases	Total number of bases that aligned to the reference, excluding bases aligning to the probe sequences. This number is the same as the number of bases aligned in the BAM file (probe sequence bases are soft-clipped). Numbers are calculated per read, and over both reads.
Total PF bases	The number of bases passing filter for the sample. Numbers are calculated per read, and over both reads.
Percent Q30 bases	The percentage of bases with a quality score of 30 or higher. Numbers are calculated per read, and over both reads.
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.
Percent aligned bases	The percentage of bases that aligned to the reference genome. Numbers are calculated per read, and over both reads.
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 reads to the targeted region divided by the number of targeted regions.
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.
SNVs, Insertions, Deletions (All)	Total number of variants present in the data set.
SNVs, Insertions, Deletions	Total number of variants present in the data set that pass the quality filters.
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.
SNVs, Insertions, Deletions (Percent found in dbSNP)	100*(Number of variants in dbSNP/Number of variants).
SNVs, Insertions, Deletions in genes	Number of variants that fall into a gene.
SNVs, Insertions, Deletions in exons	Number of variants that fall into an exon.
SNVs, Insertions, Deletions in coding regions	Number of variants that fall into a coding region.
SNVs, Insertions, Deletions in UTR regions	Number of variants that fall into an untranslated region (UTR).
SNVs, Insertions, Deletions in splice site regions	Number of variants that fall into a splice site region.
Stop gained SNVs, Insertions, Deletions	Number of variants that cause an additional stop codon.
Stop lost SNVs, Insertions, Deletions	Number of variants that cause the loss of a stop codon.
Non-synonymous SNVs, Insertions, Deletions	Number of variants that cause an amino acid change in a coding region.
Synonymous SNVs	Number of variants that are within a coding region, but do not cause an amino acid change.
Frameshift Insertions, Deletions	Number of variants that cause a frameshift.