In rare cases, when a read maps with an unaligned end to an insertion in the PointFinder database, a resistance-causing insertion may be reported that is not supported by the data. This only occurs when the read maps with a higher mapping score to another variant.
To illustrate with an example: a read maps to the resistance-causing variant ins_28_AAA with an unaligned end (in lowercase letters), as shown below. The AAA insertion is only part of the variant in the read, and the variant is, correctly, not reported.
Evaluation of ins_28_AAA
GTGGCACGACGTGCCCGCGTTGACGCC GAGCTAGTCCGGCGGGGCCTGGC <- Wildtype GTGGCACGACGTGCCCGCGTTGACGCCAAAGAGCTAGTCCGGCGGGGCCTGGC <- resistance causing variant ins_28_AAA GTGGCACGACGTGCCCGCGTTGACGCCAAAaaaaaaa <- read
Although the read maps to the resistance causing variant, it may contain additional resistance-causing variants. In this example, the algorithm evaluates whether ins_30_AA is also present. Again, the AA insertion is only part of the variant in the read, but for this additional variant, the variant is reported when it should not be.
Evaluation of ins_30_AA
GTGGCACGACGTGCCCGCGTTGACGCCGA GCTAGTCCGGCGGGGCCTGGC <- Wildtype GTGGCACGACGTGCCCGCGTTGACGCCGAAAGCTAGTCCGGCGGGGCCTGGC <- resistance causing variant ins_30_AA GTGGCACGACGTGCCCGCGTTGACGCCAAAaaaaaaa <- read
This issue affects CLC Microbial Genomics Module and CLC Microbial Genomics Server Extension 23.0.3 and earlier, 24.0 and 24.0.1.
This issue was addressed in CLC Microbial Genomics Module and CLC Microbial Genomics Server Extension 23.0.4 and 24.1.