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 %}
{% for row in missing_rbs %} {% if "None found" in row.__message %} {% endif %} {% endfor %}
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

{% for codon_key in weird_starts_overall_sorted_keys %} {% endfor %}
Start Codon Count
{{ codon_key }}{{ weird_starts_overall[codon_key] }}
{% for row in weird_starts %} {% endfor %}
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.

{% for row in excessive_gap %} {% endfor %}
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.

{% for row in excessive_overlap %} {% endfor %}
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.

{% for row in gene_model %} {% endfor %}
ID Exon CDS Message
{{row[0]}} {{row[1].location}} {{row[2].location}} {{row[3]}}