Sample Summary Report
The RNA Amplicon app creates a summary metrics file, summary.csv, for each sample included in the analysis.
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Statistic |
Definition |
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Sample ID |
IDs of samples reported on in the file. |
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Sample Name |
Names of samples reported on in the file. |
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Run Folder |
Run folders for samples reported on in the file. |
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Analysis Folder |
Output folder of the analysis. |
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Reference Genome |
Reference genome specified in the manifest. |
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Metrics Version |
PUMA metrics version. |
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Metrics deliverable |
Metrics to output. |
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Manifest |
The manifest file used for analysis. This file specifies the targeted regions for the aligner. |
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Number of amplicon regions. |
The number of amplicon regions sequenced. |
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Total length of target regions. |
Total length of sequenced bases in the target region. |
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Number of amplicon regions with at least 1 read |
The number of amplicon regions with at least one read. |
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Number of amplicon regions with at least 10 reads |
The number of amplicon regions with at least 10 reads. |
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Number of amplicon regions with at least 100 reads |
The number of amplicon regions with at least 100 reads. |
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Number of amplicon regions with at least 1K reads |
The number of amplicon regions with at least 1000 reads. |
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Number of amplicon regions with at least 10K reads |
The number of amplicon regions with at least 10,000 reads. |
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Percent amplicon regions with at least 1 read |
Percent amplicon regions with at least one read. |
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Percent amplicon regions with at least 10 reads |
Percent amplicon regions with at least 10 reads. |
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Percent amplicon regions with at least 100 reads |
Percent amplicon regions with at least 100 reads. |
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Percent amplicon regions with at least 1K reads |
Percent amplicon regions with at least 1000 reads. |
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Percent amplicon regions with at least 10K reads |
Percent amplicon regions with at least 10,000 reads. |
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Number of fusions passing filter |
The number of fusions passing filter. |
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Total on-target aligned reads |
The number of on-target aligned reads. |
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Total on-target aligned reads read 1 |
The number of on-target aligned reads in Read 1. |
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Total on-target aligned reads read 2 |
The number of on-target aligned reads in Read 2. |
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Percent on-target aligned reads |
The percentage of on-target aligned reads. |
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Percent on-target aligned reads read 1 |
The percentage of on-target aligned reads in Read 1. |
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Percent on-target aligned reads read 2 |
The percentage of on-target aligned reads in Read 2. |
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Percent on-target PF reads |
The percentage of on-target PF reads. |
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Percent on-target PF reads read 1 |
The percentage of on-target PF reads in Read 1. |
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Percent on-target PF reads read 2 |
The percentage of on-target PF reads in Read 2. |
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Total PF reads |
The number of reads passing filter for the sample. |
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Total PF read 1 |
The number of reads passing filter in Read 1. |
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Total PF read 2 |
The number of reads passing filter in Read 2. |
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Total aligned reads |
Total number of reads passing filter present in the data set that are aligned to the reference genome. Numbers are calculated per read, and over both reads. |
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Total aligned read 1 |
The number of reads passing filter in read 1 that are aligned to the reference genome. |
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Total aligned read 2 |
The number of reads passing filter in read 2 that are aligned to the reference genome. |
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Percent aligned reads |
Percentage of reads passing filter that are aligned. Numbers are calculated per read, and over both reads. |
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Percent aligned read 1 |
Percentage of reads passing filter in Read 1 that are aligned. |
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Percent aligned read 2 |
Percentage of reads passing filter in Read 2 that are aligned. |
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Total aligned on-target bases |
The number of on-target aligned bases. |
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Total on-target aligned bases read 1 |
The number of on-target aligned bases in Read 1. |
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Total on-target aligned bases read 2 |
The number of on-target aligned bases in Read 2. |
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Percent on-target aligned bases |
The percentage of on-target aligned bases. |
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Percent on-target aligned bases read 1 |
The percentage of on-target aligned bases in Read 1. |
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Percent on-target aligned bases read 2 |
The percentage of on-target aligned bases in Read 1. |
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Percent on-target PF bases |
The percentage of on-target PF bases. |
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Percent on-target PF bases read 1 |
The percentage of on-target PF bases in Read 1. |
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Percent on-target PF bases read 2 |
The percentage of on-target PF bases in Read 2. |
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Total PF bases |
The number of bases passing filter for the sample. Numbers are calculated per read, and over both reads. |
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Total PF bases read 1 |
The number of bases passing filter for Read 1. |
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Total PF bases read 2 |
The number of bases passing filter for Read 2. |
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Percent Q30 bases |
The percentage of bases with a quality score of 30 or higher. Numbers are calculated per read, and over both reads. |
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Percent Q30 bases read 1 |
The percentage of bases with a quality score of 30 or higher in Read 1. |
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Percent Q30 bases read 2 |
The percentage of bases with a quality score of 30 or higher in Read 2. |
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Total aligned bases |
Total number of bases present in the data set that aligned to the reference genome, including the probe sequences (sum of total probe bases and total aligned nonprobe bases). Numbers are calculated per read, and over both reads. |
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Total aligned bases read 1 |
Total number of bases present in Read 1 that aligned to the reference genome, including the probe sequences (sum of total probe bases and total aligned nonprobe bases). |
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Total aligned bases read 2 |
Total number of bases present in Read 2 that aligned to the reference genome, including the probe sequences (sum of total probe bases and total aligned nonprobe bases). |
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Percent aligned bases |
The percentage of bases that aligned to the reference genome, including the probe sequences (total aligned bases). Numbers are calculated per read, and over both reads. |
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Percent aligned bases read 1 |
The percentage of bases in Read 1 that aligned to the reference genome, including the probe sequences (total aligned bases). |
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Percent aligned bases read 2 |
The percentage of bases in Read 2 that aligned to the reference genome, including the probe sequences (total aligned bases). |
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Percent mismatches |
The average percentage of mismatches across Reads 1 and 2 over all cycles. |
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Percent mismatches read 1 |
The average percentage of mismatches in Read 1. |
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Percent mismatches read 2 |
The average percentage of mismatches in Read 2. |
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Amplicon mean coverage |
The total number of aligned reads to the target regions divided by the number of target regions. |