Output from Find Best References using Read Mapping
The tool can produce the following outputs:
- Target reference sequences. A sequence list (
) containing the best target reference sequences.
- Target reads track. A reads track (
) containing the reads mapped to the best target references. The mapping statistics in the table and report outputs are calculated from this track, which is produced in:
- The first mapping step if Remap reads to best target references is unchecked.
- The final mapping step if Remap reads to best target references is checked.
- Host reads track. If relevant, a reads track () containing the reads mapped to the host references.
- Table. A table (
) summarizing mapping statistics for the best target references.
- Report. A report (
) summarizing mapping statistics and details for the best target references.
Note that the mapping statistics used for filtering the references as configured in the Refinement dialog can differ from those in the table and report outputs. Therefore, some best target references may appear not to satisfy one or more filters, even though it passed filtering. For additional post-filtering, we recommend Filter on Custom Criteria.
Table
The table contains one row per best target reference. When Treat each assembly ID as a reference is chosen, the table also contains one assembly summary row for each assembly ID, summarizing all target references with that assembly ID. The rows are ordered so that the target references belonging to an assembly are listed immediately after the corresponding assembly summary row. The columns are described in table 8.1.
Report
The report has the following sections.
Summary. Contains the following subsections:
- Mapping summary. A table with the following information. Percentages are relative to the number of input reads.
- Input reads. The number of reads in the input sequence list(s).
- Reads mapped to target references. The number and percentage of reads that mapped to a target reference.
- Reads mapped to host references. If relevant, the number and percentage of reads that mapped to the host references.
- Unmapped reads. The number and percentage of reads that did not map in the first mapping step.
- Target references summary. A table with the following information:
- Identified target references. The number of target references or assembly, as relevant, with at least one mapped read.
- Discarded target references. The number of target references or assembly, as relevant, discarded during filtering.
- Best target references. The number of best target references or assembly, as relevant.
- Target references mapping summary. A table with the following information. Percentages are relative to the number of reads mapped to target references.
- Reads mapped to target references. The number of reads that mapped to a target reference.
- Reads mapped to best target references. The number and percentage of reads that mapped to the best target references.
- Reads mapped to discarded target references. The number and percentage of reads that mapped to target references discarded during filtering.
- Reads excluded due to maximum coverage. Present only when using the High-sensitivity mapping option. The number of reads excluded during downsampling before BLAST refinement because local coverage exceeded Maximum coverage. These reads are excluded only from the BLAST refinement and are still used in the remaining mapping steps.
If this value is high, it may indicate issues with the input data, such as insufficient trimming or many reads from low-complexity regions. We recommend inspecting the quality of the input reads and the coverage distribution across the best target references.
- Best target reference. A table summarizing the highest-ranked reference or assembly, as relevant, with information similar to the standalone table output (table 8.1).
Best target references. A table summarizing the best target references and, where relevant, assembly summary rows, with information similar to the standalone table output (table 8.1).