Phage {{record_name}}

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 %} {% endfor %}
Feature Type ID Location Error Upstream (-{{upstream_max}} .. -{{upstream_min}})
{{row.type}} {{row.id}} {{row.location.start}}..{{row.location.end}} [{{row.strand}}] {{row.__message}} {{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 %}
Feature Type ID Location Error
{{row.type}} {{row.id}} {{row.location.start}}..{{row.location.end}} [{{row.strand}}] {{row.__error}}

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]}} ORFs 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].id}} ({{row[0].location}}) {{row[1].id}} ({{row[1].location}}) {{row[2]}}..{{row[3]}} {{row[3] - row[2]}} bp

Antisense Genes

Possible Morons {{morons_good}} / {{morons_good + morons_bad}} (Doesn't count towards score)

{% for row in morons %} {% endfor %}
Feature RBS Surrounding Features
{{row[0].id}} {{row[3]}} {% for x in row[1] %} {{ x | nice_strand }} {% endfor %} {{ row[0].strand | nice_strand }} {% for x in row[2] %} {{ x | nice_strand }} {% endfor %}

Annotation Issues

Missing Product Tags {{missing_tags_good}} / {{missing_tags_good + missing_tags_bad}}

{% for row in missing_tags %} {% endfor %}
Feature Qualifiers
{{row.id}} {% for key in row.qualifiers %} {{ key }}
    {% for value in row.qualifiers[key] %}
  • {{value}}
  • {% endfor %}
{% endfor %}