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Example 1: ybaL mutation at 475,292 in REL8593A sample.
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
Chromosome names MUST MATCH EXACTLY in all input data files - reference genome, genes, SNP databases, etc. Don't assume these all follow one convention. It's common to find chromosomes simply numbered 1, 2, 3, etc. It's also common to find them named "chr1", "chr2", "chr3"...