Table 1.

Average number of correctly detected simulated differences by NucDiff with different parameter settings and QUAST

Difference	Truth	Default	c30	c120	l10	l65	b80	b350	QUAST-like	QUAST
insertion	1650	1634	1634	1634	1634	1634	1632	1634	1634	858
deletion	1719	1678	1678	1678	1677	1678	1679	1676	1674	465
duplication	251	136	122	150	136	136	137	124	136	196
tandem_duplication	60	57	57	57	57	57	60	54	57	57
collapsed_repeat	58	53	53	53	53	53	54	51	53	53
collapsed_tandem_repeat	59	55	55	55	55	55	56	53	55	55
relocation	217	127	142	108	127	127	136	112	127	130
relocation-insertion	13	13	13	13	13	13	13	13	13	13
relocation-insertion_ATGC	13	13	13	13	13	13	13	13	13	13
relocation-inserted_gap	13	13	13	13	13	13	13	13	13	13
relocation-overlap	13	13	13	13	13	13	13	13	13	12
translocation	111	50	57	43	50	50	50	50	50	62
translocation-insertion	13	12	12	12	12	12	12	12	12	13
translocation-insertion_ATGC	13	13	13	13	13	13	13	13	13	13
translocation-inserted_gap	13	13	13	13	13	13	13	13	13	13
translocation-overlap	13	13	13	13	13	13	13	13	13	11
inversion	534	530	530	528	529	530	531	526	530	528
reshuffling	2585	2585	2585	2585	2585	2585	2585	2585	2585	2536
substitution	115	81	81	81	80	81	89	68	81	84
gap	49	46	46	46	46	46	48	46	45	34
inserted_gap	21	21	21	21	21	21	21	21	20	16
mapped_seq	13	10	11	6	10	10	10	10	10	10
unaligned_sequence	13	13	13	13	13	13	13	13	13	13