TABLE 2.

Sequencing information of Polizzello samples.

Sample name	Type	Endogenous mtDNA (%)	Likely NumtS reads (%)	Mean per base depth	mtDNA coverage (%)
Pol-1	SE	1.32	0.55	121.18	91.76
Pol-2	PE	5.10	2.98	816.82	97.73
Pol-3	PE	4.00	2.64	369.31	96.47
Pol-4	SE	6.44	3.37	63.93	89.55
Pol-5	PE	6.87	3.93	138.76	96.66
Pol-6	PE	6.69	3.98	511.64	97.79
Pol-7	PE	6.70	3.98	386.28	98.12
Pol-8	PE	0.59	0.47	1.88	62.77
Pol-9	PE	7.16	4.55	319.20	96.67
Pol-10	PE	7.29	4.38	261.09	95.58
Pol-11	SE	0.25	0.13	88.64	90.72
Pol-12	PE	7.17	4.21	284.18	96.30
Pol-13	PE	5.55	3.26	590.39	96.42
Pol-14	PE	5.39	3.24	301.49	95.69
Pol-15	SE	4.52	2.53	65.74	90.48
Pol-16	PE	5.46	3.79	142.82	92.00
Pol-17	SE	5.80	2.87	75.55	91.16
Pol-18	SE	3.30	2.08	64.67	88.74
Pol-19	SE	0.30	0.21	0.24	21.61
Pol-20	SE	0.41	0.34	0.19	15.82
Pol-21	SE	1.47	0.96	56.30	89.57
Pol-22	SE	4.63	2.92	46.83	88.21
Pol-23	SE	3.40	1.91	73.45	90.14
Pol-24	PE	4.94	3.05	315.89	96.42
Pol-25	SE	4.56	2.08	89.86	90.59
Pol-26	PE	5.67	3.09	1, 190.13	98.38
Pol-27	PE	5.86	3.46	804.09	97.93
Pol-28	PE	4.71	2.94	377.70	94.93
Pol-29	SE	5.94	3.24	44.38	88.00
Pol-30	SE	0.33	0.15	110.11	92.58
Average all	–	4.39	2.58	257.09	87.63
Median all	–	5.02	2.96	129.97	92.29
Average SE	–	3.05	1.67	64.36	79.92
Median SE	–	3.35	1.99	65.21	89.86
Average PE	–	5.57	3.37	425.73	94.37
Median PE	–	5.61	3.36	344.26	96.45

Type of sequencing (PE, paired-end; SE, single-end), mitochondrial DNA (mtDNA) depth, coverage and percentage of potential endogenous mtDNA, and NumtS content are reported for each sample. Endogenous mtDNA percentage was calculated by dividing the number of uniquely mapped reads on mtDNA with mapping quality ≥ 30 with the number of raw reads before Clip&Merge process, while the percentage of likely NumtS reads is the fraction of reads ambiguously mapped to mtDNA and nuclear DNA with respect to the total number of raw reads. The average and median values were calculated for all samples and discriminating single-end from paired-end samples.