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 %}
Feature Type |
ID |
Location |
Error |
Upstream (-{{upstream_max}} .. -{{upstream_min}}) |
{% for row in missing_rbs %}
{{row.type}} |
{{row.id}} |
{{row.location.start}}..{{row.location.end}} [{{row.strand}}] |
{{row.__message}} |
{{row.__upstream}} |
{% endfor %}
Start Codon Usage
This section covers genes with unusual start codons
Start Codon |
Count |
{% for codon_key in weird_starts_overall_sorted_keys %}
{{ codon_key }} | {{ weird_starts_overall[codon_key] }} |
{% endfor %}
Feature Type |
ID |
Location |
Error |
{% for row in weird_starts %}
{{row.type}} |
{{row.id}} |
{{row.location.start}}..{{row.location.end}} [{{row.strand}}] |
{{row.__error}} |
{% endfor %}
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 |
{% for row in excessive_gap %}
{{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 %}
|
{% endfor %}
Overlapping Genes
Large gene overlaps may indicate an incorrect gene start or miscalled gene.
Feature A |
Feature B |
Shared Region |
Overlap Length |
{% for row in excessive_overlap %}
{{row[0].id}} ({{row[0].location}}) |
{{row[1].id}} ({{row[1].location}}) |
{{row[2]}}..{{row[3]}} |
{{row[3] - row[2]}} bp |
{% endfor %}
Possible Morons {{morons_good}} / {{morons_good + morons_bad}} (Doesn't count towards score)
Feature |
RBS |
Surrounding Features |
{% for row in morons %}
{{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 %}
|
{% endfor %}
Missing Product Tags {{missing_tags_good}} / {{missing_tags_good + missing_tags_bad}}
Feature |
Qualifiers |
{% for row in missing_tags %}
{{row.id}} |
{% for key in row.qualifiers %}
{{ key }}
{% for value in row.qualifiers[key] %}
- {{value}}
{% endfor %}
{% endfor %}
|
{% endfor %}