Table 1.

Step N to N + 5 of a series of extended-k-mer operations across a hypothetical truth sequence

Number of flanking bases is taken to be a small value of 2 for illustration only. At step N, the truth has an A flanked by GT and CG, this is characterized by GTACG. The read has a matching A, so a Match event is recorded/simulated. At step N + 1, the truth has a C flanked by TA and GT, this is characterized by TACGT. The read has a deleted C, so a Deletion event is recorded/simulated. At step N + 3, the truth is a length-5 T homopolymer flanked by CG and AC, this is characterized by CGT⁵AC. Over the stretch of homopolymer, one A is inserted in the read, and a insertion event is recorded/simulated.