Find Resistance with PointFinder can report a resistance-causing insertion when the variant supported by the reads is different

Issue description

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

Affected software

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.

Sample to Insight
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