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Fig. 5 | BMC Genomics

Fig. 5

From: A streamlined tethered chromosome conformation capture protocol

Fig. 5

Detection of simulated structural variants by RTCC. This figure shows an analytical evaluation of feasibility for using RTCC data to detect large scale structural variations in the C. elegans genome. For this analysis, the N2 reference genome was computationally modified to simulate “model reference genomes” that differ structurally from the normal C. elegans genome. We then analyzed the data from N2 (DpnII) experiments as in Fig. 2, aligning the reads to the indicated simulated reference genome and using a 50KB window size as above. In each case, the analysis yields a footprint characteristic of the simulated rearrangement. In (a), we simulated a two-chromosome fusion: we generated a model reference genome in which chrI was artificially separated into 2 parts (I-L and I-R), each 7.53MB long. Execution of our analysis pipeline resulted in visible evidence for a high level of contacts between the artificially created right tip of I-L and the artificially created left tip of I-R of the model reference genome, which are “fused” in the N2 genome. In (b), we simulated a reciprocal translocation by creating a model reference genome in which segments of chromosomes II and IV were virtually recombined. The simulated recombination was created in the middle of a TC5 transposable element (3171bp long) present in multiple copies in the genome to simulate a rearrangement that would have presented detection challenges by standard methods. The “translocation” in the N2 data (relative to the model reference genome) is evident on the plot, by the distinct accentuation of contacts between II-L and II-R and IV-L and IV-R. In (c), we generated a model reference genome in which a large inversion (4MB in length) was virtually introduced on chromosome I. Evidence for inversion is visible on the plot

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