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  • Inconsistent alignment at indels
    1. Example 1: ybaL mutation at 475,292 in REL8593A sample.
    2. Example 2:
  • Misalignment across structural variants
    1. Example 1: gltB mutation at 3,289,962 in REL8593A sample?
    2. Example 2: rbs mutation at 3,289,962 in REL8593A sample?
  • Mismapping of reads not present in reference genome
  • Dark matter: repetitive genomic regions
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