- Inconsistent alignment at indels
- Example 1: ybaL mutation at 475,292 in REL8593A sample.
- Example 2:
- Misalignment across structural variants
- Example 1: gltB mutation at 3,289,962 in REL8593A sample?
- 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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