Table 1.
Publicly available Mtb WGS datasets included in PolyTB.
| Population (reference) | ENA accession number | Sample size/post-QC | Read length | Median read depth | Post-QC No. SNPs |
|---|---|---|---|---|---|
| Samara, Russia [10] | ERP000192 | 329/264 | 49 | 61 | 18,936 |
| Midlands, UK [18] | ERP000276 | 390/390 | 75 | 112 | 19,406 |
| Kampala, Uganda [52] | ERP000520 | 51/51 | 75 | 257 | 8021 |
| Global key strains [4] | ERP001731 | 171/166 | 75/100 | 97 | 29,181 |
| Bilthoven, Netherlands [19] | ERP000111 | 213/153 | 75/100 | 39 | 10,016 |
| Vancouver, Canada [17] | SRP002589* | 36/24 | 50 | 37.5 | 1026 |
| Lisbon, Portugal (J. Perdigão et al., submitted for publication) | ERP002611** | 84/81 | 100 | 104 | 6627 |
| Karonga, Malawi (J. Guerra-Assunção et al., in preparation) | ERP000436 | 353/341 | 75 | 183 | 19,285 |
| Overall | 1, 627/1470 | 74,039 |
A set of 8 whole-genome sequencing (WGS) studies available in the public domain were downloaded from the European Nucleotide Archive (ENA). All samples were sequenced at the Wellcome Trust Sanger Institute, except * at the Simon Fraser University and ** at the King Abdullah University of Science and Technology (KAUST); all data generated using Illumina Genome Analyzer II technology, except Malawi (Karonga Study), Portugal (Lisbon) and Uganda (Kampalan Study) obtained using Illumina HiSeq 2000.