Table 1.
Comparison of Sequence Data Quality Obtained From Isolates and High-Quality Enriched Specimens
| Genome | cgMLST Count | SNP Calling Accuracy, %a | Contig Count | N50b | Mean Coverage | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CSF (n = 180) | Isolates (n = 109) | CSF (n = 180) | Isolates (n = 109) | CSF (n = 180) | Isolates (n = 109) | CSF (n = 180) | Isolates (n = 109) | CSF (n = 180) | Isolates (n = 109) | CSF (n = 180) | Isolates (n = 109) | |
| Minimum | 1.94 × 106 | 2.09 × 106 | 1405 | 1562 | 95.6 | 98.8 | 63 | 94 | 7781 | 37 341 | 16 | 24 |
| Maximum | 2.55 × 106 | 2.14 × 106 | 1580 | 1581 | 99.2 | 99.% | 718 | 165 | 78 704 | 68 913 | 364 | 127 |
| Mean | 2.11 × 106 | 2.11 × 106 | 1534 | 1569 | 98.2 | 98.9 | 215 | 132 | 35 413 | 52 558 | 222 | 53 |
| ± SD | ± 90 327 | ± 10 894 | ± 44 | ± 3 | ± 0.9 | ± 0.06 | ± 119 | ± 16 | ± 12 759 | ± 6724 | ± 81 | ± 26 |
Abbreviations: cgMLST, core genome multilocus sequencing type; CSF, cerebrospinal fluid; SNP, single-nucleotide polymorphism.
a
Calling accuracy was assessed using the correlation between accuracy of allele calling for cgMLST loci and the number of loci present [13].
b
N50 is the shortest contig length that needs to be included for covering 50% of the genome.