Read summary
Contamination
These two plots show mapping summaries that can highlight potential contamination issues.
The first plot shows the percentage of reads that either map to any combined reference sequence or are unmapped.
The second plot breaks down the the alignment numbers into the specific references (host, helper plasmid, Rep-Cap plasmid, and transgene plasmid).
Truncations
This plot illustrates the frequency of start and end positions of alignments that map completely within the transgene plasmid ITR-ITR region, helping to identify potential truncation hotspots.
ITR-ITR coverage
For each transgene reference, sequencing depth is calculated for both forward and reverse mapping alignments.
AAV Structures
The numbers of different of the various AAV transgene genome types identified in the sample(s) are summarised here.
A detailed report containing more granular genome type assignments per read can be found at: `output/<sample_id>/<sample_id>_aav_per_read_info.tsv`
| Assigned_genome_type | count | percentage | sample_id |
|---|---|---|---|
| Backbone contamination | 6840 | 68.4 | sample_1 |
| Partial ssAAV | 2620 | 26.2 | sample_1 |
| Full_ssAAV | 511 | 5.11 | sample_1 |
| Unknown | 29 | 0.29 | sample_1 |
| Assigned_genome_type | count | percentage | sample_id |
|---|---|---|---|
| Backbone contamination | 6840 | 68.4 | sample_2 |
| Partial ssAAV | 2620 | 26.2 | sample_2 |
| Full_ssAAV | 511 | 5.11 | sample_2 |
| Unknown | 29 | 0.29 | sample_2 |
Metadata
| Key | Value |
|---|---|
| sample | sample_1 |
| type | test_sample |
| barcode | sample_1 |
| Key | Value |
|---|---|
| sample | sample_2 |
| type | test_sample |
| barcode | sample_2 |