Following is a list of reports displayed when a secondary analysis
job is completed. The reports that display depend on the secondary analysis
protocol used.
- Some of the reports display on the Monitor
Jobs tab as a job is running and each phase of the job completes.
- The data is created by SMRT
Pipe and rendered by SMRT Portal.
- To see definitions of the terms displayed in reports, click Report Terminology.
SMRT Portal Reports
General - Overview
- Displays a summary of coverage, mapping and variant data for the
secondary analysis job.
- To display the full report:
Click within the small report image.
General - Filtering Report
- Displays pre- and post-filter read length and read quality. Filtering removes reads that do
not meet the read quality and read length parameters set by the user.
- Note: Read Quality is a trained
prediction of a read’s mapped accuracy based on its pulse and base
file characteristics (peak signal-to-noise ratio, average base QV,
interpulse distance, and so on).
- Report
Terminology
General - Subread Filtering Report
- Displays the number of subreads versus subread length.
General - Barcoding Report
- Displays statistics on reads and bases associated with individual
barcodes.
- Report
Terminology
General - Reads of Insert Report
Diagnostic - Adapters Report
- Displays the median distance between observed adapters per pre-filter
read.
- Combined, % Adapter Dimer (0-10bp)
and % Short Insert (11-100bp)
represent adapter dimer contamination.
- Report
Terminology
Diagnostic - Loading Report
Diagnostic - Spike-in Control Report
- Displays the read length and accuracy of control versus sample
reads. If sample preparation was performed correctly, the two should
be similar.
- Note: The
Spike-In control is specified in RS Remote,
when designing the run.
- Report
Terminology
Resequencing - Mapping Report
- Mapping is local alignment
of a read or subread to a reference sequence.
- Displays the total number of reads versus the number of mapped
reads.
- Displays the read accuracy.
- Displays reads versus the aligned length, in base pairs.
- Displays single-movie metrics.
- Report
Terminology
Resequencing - Coverage Report
- Displays depth of coverage across references, as well as depth
of coverage distribution.
- Report
Terminology
Analysis - Variants Report
Analysis - Top Variants Report
- Displays the position, type and coverage of the top 100 variants,
sorted on confidence.
- Report
Terminology
Assembly - Pre-Assembly Report
Assembly - Polished Assembly Report
- Displays statistics on the contigs from the de
novo assembly that were corrected by Quiver.
- Report
Terminology
Assembly - Iterations Report
- Displays the number of contigs over the number of assembly iterations.
- Displays the number of new overlaps over the number of assembly
iterations.
- Report
Terminology
Assembly - Corrections Report
- Displays statistics on assembly corrections (insertions, deletions,
substitutions) across contigs.
- Report
Terminology
Assembly - Top Corrections Report
- Displays statistics on the assembly corrections (insertions, deletions,
substitutions) with the highest confidence.
- Report
Terminology
Hybrid Assembly - Final Assembly Report
- Displays statistics on the initial and final scaffolds, contigs,
and gaps.
- Report
Terminology
Hybrid Assembly - Assembly Iterations Report
- Displays the number of scaffolds over the number of hybrid assembly
iterations.
- Displays the number of linking reads over the number of hybrid
assembly iterations.
- Report
Terminology
Modifications - Modifications Report
- Displays base modification quality values over the number of bases.
- Displays per-stand coverage over base modification quality values.
Modifications - Motifs Report
- Displays statistics for the methyltransferase recognition
motifs detected.
- Report Terminology
Amplicons - Input Metrics Report
Amplicons - Amplicon Consensus Summary Report
IsoSeq - Classify Report
- Displays statistics on the number of three prime, five prime, and
poly-A reads.
- Report Terminology
IsoSeq - Cluster Report
Site Acceptance Test Report