Table 4. Correction for variants detected by self-alignment (Steps A and C).
| Reference SNVs a | 42156 |
| Rd alleles in NP-NN b | −42 |
| Rd-exclusive alleles c | −237 |
| Solved ambiguous Rd d | −92 |
| NP-NN-specific e | +3 |
| MAP7-specific in NP-NN f | +3 |
| Rd-RR specific g | +40 |
| Adjusted validation set h | 41821 |
a
SNVs detected by Mauve whole-genome alignment of the reference Rd and 86-028NP genomes.
b
Alleles shared between Rd-RR and NP-NN, due to introduction of MAP7 antibiotic resistance alleles.
c
Alleles shared between Rd-RR and NP-NN that are variant only in the Rd reference.
d
Alleles shared that were originally non-ACGT bases in the Rd reference.
e
Alleles found only in NP-NN.
f
Alleles in NP-NN that are MAP7-specific.
g
Alleles found only in Rd-RR.
h
Final set of SNVs used for cross-validation (Table 5).