Table 5. Cross-validation of SNVs detected by reciprocal alignment (Steps B and C).
| Rd-RR to NP | NP-NN to Rd | |
| Adjusted validation set a | 41,821 | |
| Detected variants b | 38,770 | 39,049 |
| Validated variants c | 37,915 | 38,048 |
| False negatives d | 3,634 | 3,711 |
| Ambiguous e | (1537) | (1538) |
| Unmapped f | (2097) | (2173) |
| False positives g | 809 | 955 |
| Cross-validated h | 37,201 (88.9%) | |
a
SNVs found by whole-genome alignment after correcting for Step A (Table 4).
b
Unambiguous SNVs detected by reciprocal alignment.
c
SNV detected by reciprocal alignment, and also found by whole-genome alignment.
d
SNV not detected by reciprocal alignment, but found by whole-genome alignment.
e
False negative due to SNV having an ambiguous base assignment.
f
False negative due to SNV missing from the reciprocal alignment.
g
SNV detected by reciprocal alignment, but not found by whole-genome alignment.
h
SNV detected by both reciprocal alignments and also whole-genome alignment (total % cross-validation in parentheses).