TABLE 2.

Properties of the 140 in silico mock communities averaged over the 10 replicates from each class.

ANI similarity	Species diversity	Strain diversity	ANI to closest reference genome (%)	AF to closest reference genome (%)#	No. species	Strains per species	Species abundance (%)
Identical: 100%	Medium	Single	100	100	106 ± 15.8	1	26.8 to 3.3 × 10–4
Identical	Medium	Multiple	100	100	92 ± 22.5	2.6 ± 0.16	62.9 to 9.0 × 10–5
Identical	High	Single	100	100	490 ± 96.0	1	26.9 to 1.9 × 10–6
Identical	High	Multiple	100	100	505 ± 74.8	2.5 ± 0.07	13.2 to 6.1 × 10–6
High: [99%, 99.75%]	Medium	Single	99.4 ± 0.22	94.5 ± 3.02	99 ± 21.3	1	38.0 to 2.4 × 10–4
High	Medium	Multiple	99.3 ± 0.22	94.4 ± 3.06	106 ± 29.7	4.7 ± 0.33	39.4 to 3.2 × 10–4
High	High	Single	99.4 ± 0.22	94.5 ± 2.93	499 ± 86.1	1	60.3 to 1.6 × 10–5
High	High	Multiple	99.3 ± 0.22	94.4 ± 3.00	450 ± 116	4.0 ± 0.32	18.4 to 1.3 × 10–5
Moderate: [97%, 99%)	Medium	Single	98.3 ± 0.54	90.9 ± 4.41	104 ± 24.3	1	62.3 to 2.3 × 10–4
Moderate	Medium	Multiple	98.4 ± 0.52	91.2 ± 3.94	106 ± 19.6	4.7 ± 0.16	29.6 to 3.2 × 10–4
Moderate	High	Single	98.3 ± 0.54	90.8 ± 4.23	509 ± 58.6	1	23.2 to 2.8 × 10–5
Moderate	High	Multiple	98.3 ± 0.53	91.1 ± 4.19	532 ± 70.9	3.8 ± 0.26	10.0 to 9.2 × 10–6
Low: [95%, 97%)	Medium	Single	96.4 ± 0.50	87.9 ± 4.56	93 ± 32.9	1	80.5 to 2.8 × 10–4
Low	Medium	Multiple	96.3 ± 0.52	88.0 ± 4.33	109 ± 26.6	3.2 ± 0.23	36.6 to 1.4 × 10–4

^#AF, alignment fraction, i.e., percentage of orthologous regions shared between two genomes.