BACoN report

bacon_potato · 2026-10-08T12:14:28 · BACoN 0.3.8 · last run took 0.1 s, not counting reused steps

Metadata from lineages.tsv: 1 column (lineage); 28 of 28 samples have a value. The figures are coloured by lineage (a colour and a shape for each value, the same in every figure and table).

Samples

faileddepth below 20x or length outside 0.8–1.2x the referenceN basesClick a column to sort.

Tree

Figure 3. SKA2 SNPs; FastTree, midpoint-rooted and ladderized. Numbers on the internal branches are supports. Markers and the muted text after the names give each genome's lineage: each value has a colour and a shape of its own, as in the legend of the heatmap below (a hollow circle: no value). The scale bar is in substitutions per SNP site, with the equivalent number of SNPs.

SNP distances

Figure 4. Pairwise SNP distances, in tree order. Colour classes are spread on a log scale over the range of the distances (legend); hover a cell for the exact distance of its pair. The inner grey bands on both axes and the blocks on the right mark the groups of identical genomes; the outer bands give each genome's lineage as a marker, a colour and a shape for each value (legend; a hollow circle: no value).

Identical genomes

No SNP between any two genomes of a group (positions with N or a gap are not compared).

• group 1 (11): 12_22_134, Alaska, Amur, Argo, Bravo, Gornyak, Irbitskiy, Kamenskiy, Mishka, Otrada, Utro_ranneye
• group 2 (10): 14_6_3, 16-35-5, 16_1_2, Bagira, Bankir, Iskra, Luks, Shah, Terra, Zdraven
• group 3 (4): 14_4_1, 16_4_3, Baron, Start
• group 4 (2): 15-27-1, Legenda

Genomes of each group by lineage (the reference has no value):

29 genomes, 6 distinct at the SNP sites compared.

Genome map

Figure 5. SNP positions along the reference (135 records of the VCF, 6 with a missing call in at least one of the 28 genomes). Hover a tick for the position, the alleles and the number of genomes with the alternate allele, with the gene, its context and the effect of the SNP. Ticks closer than 159 bp are merged; hover shows the SNPs of a tick. Genes from NC_008096.2.gb (141): the + strand above the centre line, the − strand below; hover a gene for its name and coordinates. Genes with 2 or more SNPs are labelled. The band above the genes shows the LSC/IRb/SSC/IRa regions from the annotated inverted repeats. The N track sums the N bases of the 28 templated assemblies per 1 kb (log scale). Positions are approximate: the consensus follows the reference coordinates, but its insertions and deletions shift the positions after them (an assembly whose length differs from the reference's by up to 5% is rescaled to it; one differing by more is counted at its own positions).

SNPs

135 SNPs on the annotated sequences: 91 in the LSC, 7 in IRb, 31 in the SSC, 6 in IRa. 57 in coding sequences (30 synonymous, 26 missense, 1 stop retained); 14 in introns; 2 in rRNA genes; 3 in pseudogenes; 1 in other genes; 59 intergenic (a SNP where genes overlap is counted for each). Genes with the most SNPs: ndhA (7), ycf1 (7), ndhF (6), atpA (4), matK (4). Click a column to sort.

Methods

Reads aligning to the reference (NC_008096.2.fasta, 155,296 bp) were extracted with minimap2 2.31-r1302 (-x map-ont). Reads shorter than 500 bp were discarded and the best 95% were kept, up to 100x of the reference length, with Filtlong 0.3.1. Each sample was assembled by reference-guided consensus: reads were aligned to the reference with minimap2 and the consensus called with samtools consensus 1.24 (-X r10.4_sup, minimum depth 3; positions with less support, or where the reads disagree, are N). SNPs were identified with SKA2 0.5.1 from split 31-mers present in all genomes (core SNPs). Pairwise SNP distances count the positions where both genomes have a nucleotide and they differ. The SNPs of each genome relative to the reference were written to a VCF file by mapping the split k-mers to the reference with ska map 0.5.1. A tree was built on the SNP alignment with FastTree 2.2.0 (GTR, SH-like supports from 100 resamples) and rooted at its midpoint. Genes were read from the annotation NC_008096.2.gb; the effect of each SNP on the coding sequences (codon and amino-acid change) was derived by BACoN with translation table 11. The LSC/IRb/SSC/IRa regions were derived from the annotated inverted repeats. The analysis was run with BACoN 0.3.8 (https://github.com/duceppemo/BACoN).

Run

Command

$CONDA_PREFIX/bin/bacon -r NC_008096.2.fasta -i reads -o bacon_potato -t 32 -p 8 --annotation NC_008096.2.gb --metadata lineages.tsv

Reference

NC_008096.2.fasta (1 sequence(s), MD5 1df29a4310752651c17606517685a681)

Annotation

NC_008096.2.gb (141 genes on 1 sequence(s); copy annotation.gb, MD5 f201588cb58de71006aeaed9ba066fbc)

Output

bacon_potato

Python

3.12.15 on Linux

Metadata

lineages.tsv (copy metadata.tsv; colours by lineage)

minimap2

2.31-r1302 — $CONDA_PREFIX/bin/minimap2

filtlong

Filtlong v0.3.1 — $CONDA_PREFIX/bin/filtlong

samtools

samtools 1.24 — $CONDA_PREFIX/bin/samtools

ska

ska 0.5.1 — $CONDA_PREFIX/bin/ska

FastTree

FastTree 2.2.0 — $CONDA_PREFIX/bin/FastTree