Aggregate Summary Report
The RNA Amplicon app creates a summary metrics file, aggregate.summary.csv,which is an aggregate of the summary.csv files for each individual sample. Select Export (CSV) next to Aggregate Summary Metrics to download the aggregate summary report.
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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 |
BamMetrics 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 1 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 1 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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Number of detected exon variants |
The number of exon variants with supporting reads. |
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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 Passing Filter (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 on-target aligned 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 manifest, including the probe sequences (sum of total probe bases and total aligned non-probe 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 in read 1 that aligned to the reference genome, including the probe sequences (sum of total probe bases and total aligned non-probe bases). |
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Total aligned bases read 2 |
Total number of bases present in in read 2 that aligned to the reference genome, including the probe sequences (sum of total probe bases and total aligned non-probe 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. |