Summary File
The DNA + RNA Amplicon App produces an overview of statistics for each sample and aggregates results in a comma-separated values (CSV) format: *.summary.csv. These files are located in the app result folder for each sample.
|
Statistic |
Definition |
|---|---|
|
Sample fingerprint |
The fingerprints of samples reported in the file. This statistic is available only when Sample ID analysis was enabled. |
|
Sample ID |
The IDs of samples reported in the file. |
|
Sample Name |
The names of samples reported in the file. |
|
Run Folder |
The file path to the run folder. |
|
Analysis Folder |
The file path to the analysis folder. |
|
Reference genome |
The reference genome selected. |
|
Metrics deliverable |
***Need description*** |
|
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 target regions |
The total length of the sequenced bases in the targeted region. |
|
Call rate |
The percentage of bases covered by PASS variants reported in the genome VCF. |
|
Autosome call rate |
The percentage of targeted bases covered by PASS variants reported on autosomes in the genome VCF file. |
|
Total on-target aligned reads |
The number of aligned reads that are on-target. |
|
Total on-target aligned reads Read 1 |
The number of aligned reads that are on-target for Read 1. |
|
Total on-target aligned reads Read 2 |
The number of aligned reads that are on-target for Read 2. |
|
Percent on-target aligned reads |
The percentage of aligned reads that are on-target. |
|
Percent on-target aligned reads Read 1 |
The percentage of aligned reads that are on-target for Read 1. |
|
Percent on-target aligned reads Read 2 |
The percentage of aligned reads that are on-target for Read 2. |
|
Percent on-target PF reads |
The percentage of reads passing filter that are on-target. |
|
Percent on-target PF reads Read 1 |
The percentage of reads passing filter that are on-target for Read 1. |
|
Percent on-target PF reads Read 2 |
The percentage of reads passing filter that are on-target for Read 2. |
|
Total PF reads |
The total number of reads passing filter for the sample. |
|
Total PF Read 1 |
The total number of reads passing filter for Read 1. |
|
Total PF Read 2 |
The total number of reads passing filter for Read 2. |
|
Total aligned reads |
The total number of reads passing filter in the data set that aligned to the reference genome. Numbers are calculated per read, and over both reads. |
|
Total aligned Read 1 |
The total number of reads passing filter that are aligned for Read 1. |
|
Total aligned Read 2 |
The total number of reads passing filter that are aligned for Read 2. |
|
Percent aligned reads |
The percentage of reads passing filter that aligned to the reference genome. Numbers are calculated per read, and over both reads. |
|
Percent aligned Read 1 |
The percentage of reads passing filter that are aligned for Read 1. |
|
Percent aligned Read 2 |
The percentage of reads passing filter that are aligned for Read 2. |
|
Total aligned on-target bases |
The number of aligned bases that are on-target. |
|
Total on-target aligned bases Read 1 |
The number of aligned bases that are on-target for Read 1. |
|
Total on-target aligned bases Read 2 |
The number of aligned bases that are on-target for Read 2. |
|
Percent on-target aligned bases |
The percentage of aligned bases that are on-target. |
|
Percent on-target aligned bases Read 1 |
The percentage of aligned bases that are on-target for Read 1. |
|
Percent on-target aligned bases Read 2 |
The percentage of aligned bases that are on-target for Read 2. |
|
Percent on-target PF bases |
The percentage of bases passing filter that are on-target. |
|
Percent on-target PF bases Read 1 |
The percentage of bases passing filter that are on-target for Read 1. |
|
Percent on-target PF bases Read 2 |
The percentage of bases passing filter that are on-target for Read 2. |
|
Total PF bases |
The number of bases passing filter for the sample. Numbers are calculated per read, and over both reads. |
|
Total PF bases Read 1 |
The total number of bases passing filter for Read 1. |
|
Total PF bases Read 2 |
The total number of bases passing filter for Read 2. |
|
Percent Q30 bases |
The percentage of bases with a quality score of 30 or higher. Numbers are calculated per read, and over both reads. |
|
Percent Q30 bases Read 1 |
The percentage of bases with a quality score of 30 or higher for Read 1. |
|
Percent Q30 bases Read 2 |
The percentage of bases with a quality score of 30 or higher for Read 2. |
|
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. |
|
Total aligned bases Read 1 |
The total number of bases that aligned for Read 1. |
|
Total aligned bases Read 2 |
The total number of bases that aligned for Read 2. |
|
Percent aligned bases |
The percentage of bases that aligned to the reference genome. Numbers are calculated per read, and over both reads. |
|
Percent aligned bases Read 1 |
The percentage of bases that aligned for Read 1. |
|
Percent aligned bases Read 2 |
The percentage of bases that aligned for Read 2. |
|
Percent mismatches |
The average percentage of mismatches across both Read 1 and 2 over all cycles. Numbers are calculated per read. |
|
Percent mismatches Read 1 |
The percentage of mismatches for Read 1. |
|
Percent mismatches Read 2 |
The percentage of mismatches for Read 2. |
|
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 (All) |
Total number of SNVs present in the data set. |
|
SNVs |
Total number of SNVs present in the data set that pass the quality filters. |
|
SNV Het/Hom ratio |
Number of heterozygous variants/Number of homozygous variants. |
|
SNV Ts/Tv ratio |
The 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 (Percent found in dbSNP) |
100* (Number of variants in dbSNP/Number of variants). |
|
SNVs in genes |
The number of variants that fall into a gene. |
|
SNVs in exons |
The number of variants that fall into an exon. |
|
SNVs in coding regions |
The number of variants that fall into a coding region. |
|
SNVs in UTR regions |
The number of variants that fall into an untranslated region (UTR). |
|
SNVs in splice site regions |
The number of variants that fall into a splice site region. |
|
Stop gained SNVs |
The number of variants that cause an additional stop codon. |
|
Stop lost SNVs |
The number of variants that cause the loss of a stop codon. |
|
Non-synonymous SNVs |
The number of variants that cause an amino acid change in a coding region. |
|
Synonymous SNVs |
The number of variants that are within a coding region, but do not cause an amino acid change. |
|
Insertions (All) |
The total number of insertions present in the data set. |
|
Insertions |
The total number of insertions present in the data set that passed the variant quality filters. |
|
Insertion Het/Hom ratio |
Number of heterozygous insertions/Number of homozygous insertions. |
|
Insertions (Percent found in dbSNP) |
100* (Number of insertions in dbSNP/Number of insertions). |
|
Insertions in genes |
The number of insertions that fall into a gene. |
|
Insertions in exons |
The number of insertions that fall into an exon. |
|
Insertions in coding regions |
The number of insertions that fall into a coding region. |
|
Insertions in UTR regions |
The number of insertions that fall into an untranslated region (UTR). |
|
Insertions in splice site regions |
The number of insertions that fall into a splice site region. |
|
Stop gained Insertions |
The number of insertions that cause an additional stop codon. |
|
Stop lost Insertions |
The number of insertions that cause the loss of a stop codon. |
|
Frameshift Insertions |
The number of insertions that cause a frameshift. |
|
Non-synonymous Insertions |
The number of insertions that cause an amino acid change in a coding region. |
|
Deletions (All) |
The total number of deletions present in the data set. |
|
Deletions |
The total number of deletions present in the data set that passed the variant quality filters. |
|
Deletion Het/Hom ratio |
Number of heterozygous deletions/Number of homozygous deletions. |
|
Deletions (Percent found in dbSNP) |
100* (Number of deletions in dbSNP/Number of deletions). |
|
Deletions in genes |
The number of deletions that fall into a gene. |
|
Deletions in exons |
The number of deletions that fall into an exon. |
|
Deletions in coding regions |
The number of deletions that fall into a coding region. |
|
Deletions in UTR regions |
The number of deletions that fall into an untranslated region (UTR). |
|
Deletions in splice site regions |
The number of deletions that fall into a splice site region. |
|
Stop gained Deletions |
The number of deletions that cause an additional stop codon. |
|
Stop lost Deletions |
The number of deletions that cause the loss of a stop codon. |
|
Frameshift Deletions |
The number of deletions that cause a frameshift. |
|
Non-synonymous Deletions |
The number of deletions that cause an amino acid change in a coding region. |