Fig. 1
From: GPU accelerated sequence alignment with traceback for GATK HaplotypeCaller
An example of an semi-global alignment of two sequences in GATK HC. R1 and R2 represent two sequences. Gaps (‘-’) at the start and end of two sequences are neglected. In the alignment, there are three kinds of operations indicating how R2 aligns with R1. ‘M’ indicates that a base in R2 aligns with a base in R1 (matches or mismatches); ‘I’ indicates that a base in R2 is not in R1; ‘D’ indicates that a base in R1 is not in R2