Table 2.

DNAdiff comparisons between Flye long read-only assemblies and hybrid assemblies

Library	Isolate name	Barcode	SNPs	Indels	% reference bases aligned	% identity
1	blc-22	bc01	3385	14 679	99.95	99.55
1	blc-23	bc02	251	9953	100	99.76
1	blc-24	bc04	3202	15 949	99.98	99.58
1	blc-25	bc05	3387	12 262	100	99.53
1	blc-26	bc06	3082	11 494	99.96	99.53
1	blc-27	bc07	3203	11 764	99.98	99.56
1	blc-28	bc08	157	12 793	99.97	99.61
1	blc-29	bc09	3309	12 036	100	99.39
1	blc-31	bc11	4070	13 861	99.98	99.51
2	blc-33	bc02	3179	15 572	99.97	99.48
2	blc-34	bc03	4942	16 498	100	99.34
2	blc-35	bc04	5488	16 499	99.9	99.36
2	blc-36	bc05	5458	16 842	100	99.35
2	blc-37	bc06	5442	16 499	99.98	99.36
2	blc-38	bc07	5460	16 559	100	99.36
2	blc-39	bc08	4311	20 783	97.82	98.45
2	blc-40	bc09	5428	16 882	99.83	99.36
2	blc-41	bc10	3064	15 975	99.93	99.37
2	blc-42	bc11	2960	15 133	100	99.44
2	blc-43	bc12	5434	16 748	100	99.35
3	blc-47	bc01	4482	19 204	99.98	99.31
3	blc-48	bc02	4352	19 444	99.99	99.3
3	blc-49	bc03	3983	18 206	99.98	99.3
3	blc-50	bc04	2615	17 537	100	99.4
3	blc-51	bc05	3728	19 560	100	99.36
3	blc-52	bc06	2645	16 326	100	99.4
3	blc-53	bc07	2645	17 567	100	99.4
3	blc-48	bc08	2580	17 145	99.95	99.39
3	blc-49	bc09	4326	19 080	99.95	99.31
3	blc-50	bc10	2607	15 458	100	99.4
3	blc-51	bc11	4406	19 273	99.99	99.31
3	blc-52	bc12	2555	17 336	100	99.4
5	blc-56	bc01	4746	19 881	99.89	98.96
5	blc-57	bc02	4174	20 993	99.46	98.56
5	blc-58	bc03	4876	20 019	99.92	99.01
5	blc-59	bc04	4649	21 014	94.41	97.93
5	blc-61	bc06	3115	14 943	100	99.45
5	blc-62	bc07	4709	15 872	100	99.33
5	blc-63	bc08	4680	15 201	99.98	99.34
5	blc-64	bc09	3051	15 973	100	99.39
5	blc-65	bc10	4212	18 101	99.36	99.22
5	blc-66	bc12	4986	21 189	98	98.61