Table 12.

Hamming Distance percentage on datasets of NA12878

Chrom.	HapCHAT	HapCol	WhatsHap	WhatsHap	HapCUT2	ReFHap	ProbHap	FastHare
			cov. 15x	cov. 20x
1	2.12	-	1.92	2.10	2.11	-	-	6.16
2	0.51	-	0.49	0.29	0.77	-	-	4.91
3	0.32	-	0.42	0.42	0.48	-	-	4.74
4	2.47	-	2.15	2.18	2.00	-	-	6.44
5	2.33	-	2.53	2.22	1.98	-	-	6.56
6	3.39	-	3.02	3.20	2.82	-	-	7.15
7	1.16	-	1.10	1.10	1.36	-	-	5.05
8	2.44	-	2.46	2.54	2.02	-	-	6.14
9	2.45	-	2.31	2.49	2.11	5.68	-	6.23
10	1.19	-	1.16	1.18	0.93	3.89	-	5.29
11	2.08	-	2.06	2.06	1.99	4.25	-	5.08
12	0.43	-	0.48	0.38	0.51	2.92	-	5.54
13	0.41	-	0.63	0.57	0.35	4.01	-	4.84
14	0.21	-	0.48	0.58	0.17	3.01	-	3.24
15	0.23	3.39	0.24	0.34	0.34	4.18	-	5.49
16	0.24	2.09	0.45	0.88	0.28	1.65	-	2.87
17	0.50	2.84	0.38	0.79	0.20	2.89	-	4.61
18	1.80	-	1.67	1.65	1.68	4.77	-	8.10
19	3.19	-	3.14	3.40	2.99	4.37	-	7.32
20	1.37	3.47	0.16	0.10	0.16	2.99	-	4.07
21	0.10	-	0.10	0.10	1.95	5.37	-	4.22
22	1.82	4.92	1.84	1.83	1.82	4.83	-	6.52

Each row corresponds to a chromosome. The dataset consists of all reads aligned to the chromosome. We report the results obtained by running the tools with maximum coverage 30 × for HapCHAT, 25 × for HapCol, 15 × and 20 × for WhatsHap. No maximum coverage was set for HapCUT2, ReFHap, ProbHap, and FastHare. The best result (lowest value) for each dataset is boldfaced