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However, the error rate of the assembly was substantial, and the coverage in some regions was very low, especially the plasmid region, where there were large regions of N’s. We started examining the regions with low coverage carefully. It turns out that in one of the mutant contigs, there was a large deletion of a single base in the WT genome. This deletion is located between two repeat sequences that also have small deletions with different lengths, and this is exactly what the low coverage sequencing showed.
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