Table 3. Summary statistics of each of the eight assemblies analyzed, with distinct values of key parameters including the minimum depth to keep a base call in the consensus sequence (–d) and the minimum coverage of a sequence to be included in the final alignment.

Key parameters	Loci (m, r)	Terminals	Aligned (bp)	Variable sites	PIS	Missing data (%)	Bootstrap (mean)
–d 2 –C 0.7	120 [1, 313]	13	540,764	118,386	16,592	63.3	66.9
–d 2 –C 0.5	268 [8, 638]	15	1,064,863	261,671	48,638	56.2	84
–d 2 –C 0.3	423 [18, 682]	16	1,442,185	411,563	93,974	46.1	97.3
–d 2 –C 0.1	618 [286, 683]	16	1,494,809	449,182	110,495	41.1	94.4
–d 3 –C 0.1	490 [39, 683]	16	1,257,452	332,727	69,297	50.6	99.1
–d 4 –C 0.1	382 [8, 672]	16	932,497	217,549	37,358	58	95.5
–d 5 –C 0.1	287 [1, 586]	16	537,866	115,958	17,078	62.3	87.3

Note:

Loci (m, r), mean and range number of recovered loci (at least partially) across all terminals; Terminals, Number of terminals in the concatenated alignment; Bootstrap (mean), mean boostrap in the concatenated phylogeny (including the same 13 terminals).