Table 4.

Reference variant calling vs. de novo variant calling. Number of variants identified using the indicated alignment strategy (as indicated in Figure 6) for variants called against the HSV1 NR-ref or the HSV1 reference (in parentheses).

Alignment Strategy	# Variants in RL	# Variants in RS	# Variants in UL	# Variants in US	# Variants Total
2a: segregating variants	5 (0)	1 (1)	19 (19)	1 (1)	26 (21)
2b: segregating variants	3 (4)	1 (3)	24 (24)	1 (1)	29 (32)
3a: divergent variants	4 (2)	2 (0)	27 (27)	1 (1)	34 (30)