TABLE 3.
Summary of SeqSero1 and SeqSero2 prediction results
| Result | No. of genomes (% of total) for: |
|||||||
|---|---|---|---|---|---|---|---|---|
| Raw reads (CDC strains) |
Raw reads (GenomeTrakr strains) |
Genome assemblies |
||||||
| SeqSero2 (k-mer) | SeqSero2 (microassembly) | SeqSero1 | SeqSero2 (k-mer) | SeqSero2 (microassembly) | SeqSero1 | SeqSero2 | SeqSero1 | |
| Expected serotypea | 292 (95.1%) | 304 (99.0%) | 303 (98.7%) | 3,014 (94.0%) | 3,020 (94.2%) | 3,018 (94.1%) | 3,305 (94.1%) | 3,043 (86.6%) |
| Unexpected serotypeb | 13 (4.2%) | 1 (0.3%) | 2 (0.7%) | 174 (5.4%) | 165 (5.1%) | 167 (5.2%) | 186 (5.3%) | 184 (5.2%) |
| Partial or no serotypec | 2 (0.7%) | 2 (0.7%) | 2 (0.7%) | 19 (0.6%) | 22 (0.7%) | 22 (0.7%) | 23 (0.7%) | 287 (8.2%) |
| All results | 307 | 307 | 307 | 3,207 | 3,207 | 3,207 | 3,514d | 3,514 |
a
The predicted serotype was considered correct when the serotype antigens detected corresponded to the antigens detected by phenotypic methods.
b
Numbers represent serotype predictions inconsistent with the annotated serotype; the accuracy of the annotated serotype is unknown for GenomeTrakr strains and genome assemblies.
c
Some or all of the expected serotype determinants were not detected.
d
CDC strains (n = 307) and GenomeTrakr strains (n = 3,207) combined.