I am running QSCORE (https://www.drive5.com/qscore/) on a number of sequence alignments. My goal is to compare a test sequence and a reference sequence, and I am using QSCORE.
I ran a batch of files and a handful out of dozens are failing. The error message I get looks more or less like this
Test seq 0 (KI123028 dna:supercontig) differs from ref seq 0 (KI123028 dna:supercontig), ref col 666=C, test=T
Please direct me to any appropriate resources if this rings a bell.