Quality assurance report

4 sample(s): 4 ok, 0 with a warning, 0 failed. BrucellaID 2.1.1, run on 2026-11-08T14:55:06-05:00.

1 Summary

Run started

2026-11-08T14:55:06-05:00

Run finished

2026-11-08T14:55:43-05:00

Operator

M-O Duceppe

Command

python3 scripts/make_example_report.py reads

2 Notes, warnings and errors

3 Samples

4 Definitions and methods

The references listed for each sample

A sample block lists the five closest reference genomes, and any other near enough to the closest that the distance does not separate them, which is the evidence the species call rests on. brucellaid_mash.tsv holds the distance to every reference of the sketch.

The species, from a MASH distance

The reads of a sample are reduced to the 1000 smallest hashes of their 21-mers, ignoring the k-mers seen fewer times than the copy threshold derived from the coverage, and that sketch is compared with the sketch of each reference genome. The distance is an estimate of the fraction of positions that differ, so 0.000024 is about 99.998% identity. The closest reference names the species, provided the reads share at least the required number of its 1000 min-hashes; below that the sample is reported as ND, because the closest genome of the set is not an answer. The reference data table above says which set this run measured against.

Why there is no biovar in this report

BrucellaID does not report a biovar, because it cannot measure one. Three things stand in the way. Hardly any reference carries a biovar at all: 7 of the 432 genomes of the default set do, because the NCBI records of the rest carry none, so 93% of the biovar-labelled B. abortus isolates of the PubMLST isolate database are of a biovar no reference has. The distance cannot separate the biovars that are there: the two B. suis biovar 2 genomes are 0.00163 apart, further than the biovar 3 genome is from one of them (0.00150). And a biovar is a phenotype that genome clustering does not track -- the best any rule from sequence type to biovar could manage over the isolate database is 66% for B. abortus and 63% for B. melitensis, because one ST spans several biovars. This report therefore shows no biovar at all, not even the ones recorded for the ST: of the 118 sequence types in the table, 42 have a single biovar on record, and showing one next to a sample invites reading it as a measurement of that sample. The counts are in the packaged mlst_st_species.tsv for anyone who wants them. For a biovar, use classical biotyping, or brucetyper, which reads the Bruce-ladder and Suis-ladder assays in silico.

The sequence type, from the alleles

The same reads are given to Seal with the alleles of the nine loci as references, counting each read for every allele it shares the highest number of 25-mers with and for no other. The allele the sample carries is therefore counted for every read of its locus, and a neighbouring allele only for the reads that fall where the two agree, so the allele with the most reads wins. No mismatch is allowed in a k-mer, because the alleles of a locus differ by as little as one base. Two alleles with the same count are reported as a tie rather than separated by a coin toss, and a locus below the minimum read count is not called.

What the ST values mean

A number is a profile that is in the table. "new" means all nine alleles were called but the combination is not in the table, which is either a genuinely new ST or a novel allele called as its nearest neighbour. "ND" means at least one locus had no call; the note says which.

How the species is decided when two are equally close

Some Brucella species are closer to each other than the variation within either of them: in the sketches that ship with BrucellaID, the closest pair of different species is always a B. canis and a B. suis: 0.00024 apart in the 16 genomes of vSNP, 0.000264 in the 432 of the default set. Where a reference of a second species is within the close-match margin of the closest one, the distance has not really chosen, and the sequence type chooses among those species, because the two share no ST. An ST is only used when enough of its isolates agree on a species, and an ST that contradicts a species the distance picked cleanly is reported as a conflict and not obeyed.

What this report does not establish

That the sample is what the label on the tube says, that the library is not a mixture of two isolates, or that the reference data is current. It establishes what the software was given, what it measured, and what it concluded from those measurements.

5 Run information

Operator

M-O Duceppe

User account

[removed]

Computer

[removed]

Operating system

[removed]

Working directory

[removed]

Started

2026-11-08T14:55:06-05:00

Finished

2026-11-08T14:55:43-05:00

Command

python3 scripts/make_example_report.py reads

Software

Parameters

Reference data

References

1. Whatmore AM, Perrett LL, MacMillan AP. Characterisation of the genetic diversity of Brucella by multilocus sequencing. BMC Microbiology 2007;7:34. doi:10.1186/1471-2180-7-34
2. Ondov BD, Treangen TJ, Melsted P, et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biology 2016;17:132. doi:10.1186/s13059-016-0997-x
3. Jolley KA, Bray JE, Maiden MCJ. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Research 2018;3:124. doi:10.12688/wellcomeopenres.14826.1
4. Bushnell B. BBTools. https://sourceforge.net/projects/bbmap/