Figure 2

Whole genome sequencing and detection of inversions. (A) In the WGS process, sequenced genome is shredded into inserts approximately 500 bp long. Each insert is sequenced from both ends (paired ends), resulting in a pair of approximately 100 bp reads. Each read is mapped independently to the reference genome, and the gap size between the insert’s edges is determined for each pair. The gap size of each read is then plotted against the read’s genomic location. As long as the actual genome is identical to the reference genome, we expect a 'ribbon' formation around 500 bp (gray diamonds). (B) Experimental paired-end data exhibiting the ribbon formation. (C) When the sequenced genome deviates from the reference genome by an inversion (represented by gray shading), inserts whose reads lie on both sides of the inversion’s edge display a unique pattern that we term a 'funnel' (two symmetric diagonal lines composed of abnormally aligned reads). (D) Experimental paired-end data exhibiting a funnel around an inversion (blue diamonds represent plus strand paired with plus strand and green diamonds represent minus strand paired with minus strand). Note that only abnormal gap size reads are shown. (E) Results of the systematic inversion detection algorithm for two strains of E. coli. Exact genomic coordinates are available in Table S1 in Additional file 1.