Table 2. Expected baseline performance for variant calling.

Group A – variants that should be detected by any variant calling pipeline; Group B – sites in which a base substitution or insertion and/or deletion should not be called.

	Number of Sites
Group A
- Base substitution variants	118
- Deletion variants	186
- Insertion variants	74
- Complex indel variants	9
Group B
- No base substitution	35
- No indel	226