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Even with clonally pure samples, NGS traces rarely show 100% sequence identity. This is because errors do occur during sequencing reactions and the subsequent data analysis.
These error rates are typically between 0.1% and 0.01%, but they can be locally elevated in regions of extreme GC content or secondary structure. Misalignment of the traces can also occur, particularly in highly repetitive sequences.
Finally, small subpopulations of sequence variants can arise during propagation of E. coli.
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