Type with MLST Scheme output
Type with MLST Scheme outputs an MLST Typing Result containing an Allele Table with the best allele match for each locus and a Novel Allele Table with any novel alleles detected. Additionally, the following outputs are also available:
- Create allele sequence list. Outputs a sequence list containing all alleles (one per locus). This comprehensive list is particularly useful for quality control or verification purposes.
- Create report. Outputs a summary report.
The MLST typing report
In the Typing result section, the "Typing" field indicates whether the sample was successfully typed or not. This outcome depends on the proportion of loci with matching alleles (either existing or novel). A sample is considered "Conclusive" when the ratio of matching loci to the total number of loci meets or exceeds the value defined by the Minimum locus presence parameter.
The Sequence Type field indicates whether the sample matches an existing sequence type in the MLST Scheme. If no match is found, the sample is classified as Novel. Matching behavior is influenced by the Comparing a known to a missing allele option, which determines how incomplete allele profiles are handled. This information is only present if the MLST Scheme contains sequence type information.
Figure 10.14: The Type with MLST Scheme report for a sample typed with a 7-loci scheme.
The Typing summary section displays a table summarizing the sequence types most similar to the analyzed sample. The table lists up to 10 sequence types ranked by proximity, along with their corresponding allelic distance from the sample. Allelic distance represents the number of differing loci between the sample and the reference sequence type. To maintain relevance, only sequence types within a maximum distance of 100 are reported.
The Typing statistics section provides an overview of the MLST typing results. It includes a table summarizing key metrics:
- Loci identified. The number of loci successfully typed, including both known and novel alleles.
- Novel alleles identified. The number of loci where a new allele sequences were detected.
- Loci not identified. The number of loci for which neither
- Locus presence (%). The percent of loci identified out of all loci contained in the MLST Scheme used for typing.
- Estimated average coverage. An estimate of sequencing depth across the typed loci, which helps assess data quality.
The Coverage distribution section includes a coverage distribution plot. The x-axis represents the average number of k-mers per locus, while the y-axis shows the frequency of loci at each coverage level. This visualization helps identify uneven coverage or potential sequencing issues.
The Closest matching sequence types section displays a table summarizing the sequence types most similar to the analyzed sample. The table lists up to 10 sequence types, along with their corresponding allelic distance from the sample, with the closest match first. Allelic distance represents the number of differing loci between the sample and the reference sequence type. To maintain relevance, only sequence types within a maximum distance of 100 are reported.
If the sample was typed using a 7-locus scheme, the report will additionally contain a section, Allele calls, which lists the specific alleles called for each of the 7 loci.
The Scheme information section contains various statistics about the MLST Scheme used for typing.
The report information can be added to a Result Metadata Table using Extend Result Metadata Table.
The MLST typing result
The MLST Typing Result contains two views: an Allele Table view with the best allele match for each locus and a Novel Allele Table view with any novel alleles detected. Switching between these views is done by clicking the buttons at the lower-left corner of the view.
Figure 10.15: The Allele Table view for an MLST Typing Result.
The Allele Table contains information about the alleles that were identified in the sample (figure 10.15). It contains the following columns:
- Locus. The name of the locus.
- Allele call. The allele that was identified for that locus. Only the best allele is reported, but if multiple alleles are tied for the first place, they will all be reported.
- Status. Indicates whether the allele call passed quality criteria. The value is either 'Pass' or 'Fail'. An allele call passes only if the Fraction of kmers equals 1.00 i.e. all kmers expected for the allele were found in the sample without any missing or ambiguous positions. This strict criterion ensures that the allele call is complete and unambiguous, reducing the risk of reporting partial or incorrect alleles.
- Fraction of kmers. The fraction of kmers of the allele that were found in the sample.
- Total kmer count. Total number of kmer hits for the allele.
- Avg kmer count. The average count of all kmers belonging to the allele that were observed in the sample. This value provides an indication of the overall coverage depth for the allele.
- Min kmer count. The minimum count among all kmers of the allele observed in the sample. This value highlights the least-supported kmer and can be useful for detecting uneven coverage or potential sequencing artifacts.
- Novel allele. Contains the string 'Novel' for novel alleles, otherwise this field is left blank.
Figure 10.16: The Novel Allele Table view for an MLST Typing Result.
The Novel Allele View (figure 10.16) displays any novel alleles detected during typing, provided that the search for novel alleles was enabled. This view is presented as a sequence list, and you can export the full sequences by clicking the Create New Sequence List button. For more on sequence lists see Working with sequence lists.
If the MLST Scheme used for typing is configured with a specified genetic code, the Gene completeness column indicates whether a novel allele starts with a start codon and ends with a stop codon; such alleles are considered complete.
If the MLST Scheme is not configured with a specified genetic code, this check cannot be performed because codon translation rules are missing, and completeness information will not be available.