Resolve the genomic basis of bacterial phase variation.

Analyze paired-end WGS from a clonal bacterial isolate to identify candidate phase-variable loci.

Paired-end isolate WGSReference-guided analysisReproducible workflow

Illustration of repeat-length variation and alternate bacterial states

START A RUN

Analyze a clonal isolate against bacterial reference candidates

ANALYSIS MODULES

Primary referencechromosome + plasmids

Iterative mappingread-supported alignment

Phase-variation signalsSSR variation · inversions

Read QC & alignment

Adapter and quality trimming with paired-end read diagnostics.

Reference-guided refinement

Iterative mapping across candidate chromosome–plasmid reference sets.

Phase-variable loci

Evidence for SSR tract variation, inversions and structural rearrangements.

RUN HISTORY

Recent analyses

No analyses submitted yet.

RESULT PREVIEW

Phase-variable loci

77Phase-variable loci43Annotated to genes

CategoryEstimated quasi-clonal population frequencyLocationGene annotation

Putative breakpoint junction5.26%CP026802.1:89834Unannotated

Inversion8.77%CP026802.1:226705Annotated gene

InsertionNACP026802.1:373342Annotated gene

Representative outputs from completed run 20260721_131110_3025636c · sample_01. Real combined subset from completed run 20260721_131110_3025636c · sample_01. Caller-specific files remain internal.

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