Phage {{record_name}}
Genome Overview
Genes
- Count: {{ genome_overview.genes.count }}
- Bases: {{ genome_overview.genes.bases }}
- Average Length: {{ genome_overview.genes.avg_len | round | int}}
- Coding Density: {{ '%0.2f' % (100 * coding_density_exact) }}%
- Composition
- A {{ genome_overview.genes.comp.A }}
- C {{ genome_overview.genes.comp.C }}
- T {{ genome_overview.genes.comp.T }}
- G {{ genome_overview.genes.comp.G }}
Overall
- %GC: {{ '%0.2f' % (100 * genome_overview.overall.gc) }}%
- Composition
- A {{ genome_overview.overall.comp.A }}
- C {{ genome_overview.overall.comp.C }}
- T {{ genome_overview.overall.comp.T }}
- G {{ genome_overview.overall.comp.G }}
Gene Starts
Genes Missing RBS {{missing_rbs_good}} / {{missing_rbs_good + missing_rbs_bad}}
The following genes have issues with their RBS.
{% if not rbss_annotated %}Since you have not annotated any possible RBSs, this does not count off from your overall score.
{% endif %}ID | Location | Error | Upstream (-{{upstream_max}} .. -{{upstream_min}}) |
---|---|---|---|
{{row | nice_id | decode}} | {{row.location.start}}..{{row.location.end}} [{{row.strand}}] | None found | {{row.__upstream }} |
Start Codon Usage
This section covers genes with unusual start codons
Start Codon | Count |
---|---|
{{ codon_key }} | {{ weird_starts_overall[codon_key] }} |
ID | Location | Error |
---|---|---|
{{row | nice_id| decode}} | {{row.location.start}}..{{row.location.end}} [{{row.strand}}] | {{row.qualifiers.get('note', [])}} |
Intergenic Gaps
Phage genomes are under pressure to maintain high coding density. Large intergenic gaps may be a sign of incorrect gene starts or missing genes.
Region | Size | Bounding Gene Transcription Direction | Message |
---|---|---|---|
{{row[0]}} .. {{row[1]}} | {{row[1] - row[0]}} | {{row[2] | nice_strand}} {{row[3] | nice_strand}} | {% if row[4] == 0 %} {% else %} {{row[4]}} possible genes found in this region {% endif %} |
Overlapping Genes
Large gene overlaps may indicate an incorrect gene start or miscalled gene.
Feature A | Feature B | Shared Region | Overlap Length |
---|---|---|---|
{{row[0] | nice_id | decode}} ({{row[0].location}}) | {{row[1] | nice_id | decode}} ({{row[1].location}}) | {{row[2]}}..{{row[3]}} | {{row[3] - row[2]}}bp |
Gene Model Issues
These issues are mostly derived from how Apollo handles the gene model.
ID | Exon | CDS | Message |
---|---|---|---|
{{row[0]}} | {{row[1].location}} | {{row[2].location}} | {{row[3]}} |