Table 1.
Summary of the V. cholerae O139 genome assemblies generated in this study.
| Internal sequence ID (PacBio) | Sample Name | CTXφ present? | Accession (PacBio reads) | Accession (closed chromosomal assembly) | Accession (Illumina reads) | Genome Size (bp) | Average coverage of de novo assembly with long reads (X) | Coverage of N16961 (%) | Number of SNVs relative to N16961 |
|---|---|---|---|---|---|---|---|---|---|
| 48853_F01 | MP_070116 | No | ERR1716489 | LT992490-LT992491 | ERR568405 | 4123525 | 165.76 | 58.5 | 122865 |
| 48853_G01 | P_0684000 | Yes | ERR1716490 | LT992486-LT992487 | ERR568406 | 4092641 | 170.56 | 97 | 271 |
| 48853_H01 | ICVB_2236_02 | Yes | ERR1716491 | LT992488-LT992489 | ERR568407 | 4092645 | 147.29 | 97 | 270 |
| 48853_A02 | SMIC_67_01 | Yes | ERR1716492 | LT992492-LT992493 | ERR568408 | 4092644 | 165.65 | 97 | 274 |
The accession numbers for both the long-read sequences and assemblies generated in this study, and the original short reads used for assembly polishing, SNV calling, and phylogenetic analyses (see Methods) are reported. The SNV counts reported do not account for the removal of recombinogenic sequences, since the non-toxigenic isolate was not included in the recombination analysis. Average coverage values taken from de novo HGAP assemblies.