Sequence utilities / GC content sliding window
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The top chart shows GC percentage per window; the dashed line is the GC% of the whole sequence. Stretches far from the average may be acquired DNA (prophages, genomic islands), rRNA operons, or sequencing/assembly artefacts.
The lower chart shows GC skew = (G − C)/(G + C). In bacterial genomes the leading strand is G-rich, so skew changes sign at the replication origin and terminus; the minimum and maximum of the cumulative skew often mark the origin and terminus respectively.
Larger windows give smoother curves, smaller windows show local detail; the step sets the density of points. The table lists the 1-based start and end of every window.
GC% counts only A/C/G/T; N and other ambiguity codes are excluded from the denominator.
GC skew and cumulative skew: Lobry 1996 (Mol Biol Evol 13:660); Grigoriev 1998 (Nucleic Acids Res 26:2286).
Up to 20,000 windows; for a complete bacterial genome use a step of 1 kb or more.
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