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Figure 4 | BMC Genomics

Figure 4

From: Distinguishing low frequency mutations from RT-PCR and sequence errors in viral deep sequencing data

Figure 4

Genome Coverage. The read coverage for each of the samples across the 11,278 bp plasmid genome: Seq (blue), PCR-Low (red), PCR-High (green) and RT-PCR (purple). The peaks correspond to the ends of DNA fragments, which are over-represented in the data set, presumably due to sonication bias; as can be seen the Seq sample operates on a slightly different section of the genome (Figure 2) but with substantial overlap with the PCR amplified samples. The two regions of the genome that are used for direct comparison between all samples are highlighted with dashed black boxes, which avoid the regions with large and potentially biased coverage spikes at the ends of DNA fragments and primer regions. The Seq control (blue) suffers a drop in coverage at around position 2,500 due to a large poly C tract that is found in all FMDV genomes, and which is problematic for both PCR and sequencing.

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