Appendix 2—table 2. Definitions of parameter regimes referenced in Appendix 1—figure 3 and Appendix 1—figure 4.

Parameter	‘Lenient’ parameter set value	‘Selected’ parameter set value	‘Strict’ parameter set value
Minimum alignment length	100 bp	300 bp	1 kbp
Insertion/deletion threshold	30 bp	30 bp	30 bp
DBSCAN epsilon (minimum clustering distance)	100 bp	1 kbp	1.4 kbp
Minimum read support	1	3	5
Majority voting?	No	Yes	Yes