Table 1 General genome features of strains
From: Comparative genomics of whole-cell pertussis vaccine strains from India
Feature | Vaccine Strains | Clinical Isolates | Reference Strain | |||||
|---|---|---|---|---|---|---|---|---|
Vaccine | WCV | WCV | WCV | WCV | ACV | Â | Â | Â |
Strains | J445 | J446 | J447 | J448 | BP 165 | BPD1 | BPD2 | Tohama –I |
Size (bp) | 4,128,984 | 4,140,370 | 4,257,407 | 4,386,396 | 4,101,762 | 4,126,211 | 4,104,911 | 4,086,189 |
G + C Content | 67.72 | 67.71 | 67.77 | 67.82 | 67.71 | 67.12 | 67.14 | 68.12 |
Genes | 3940 | 3951 | 4069 | 4192 | 3893 | 4004 | 3985 | 3856 |
Coding sequences | 3876 | 3887 | 4005 | 4128 | 4035 | 3941 | 3921 | 3806 |
Pseudo-genes | 231 | 237 | 238 | 246 | 307 | 384 | 359 | 359 |
rRNA (5S, 16S, 23S) | 3, 3, 3 | 3, 3, 3 | 3, 3, 3 | 3, 3, 3 | 3,3,3 | 3,3,3 | 3,3,3 | 3,3,3 |
tRNA | 51 | 51 | 51 | 51 | 49 | 51 | 51 | 51 |
IS481 | 255 | 252 | 266 | 273 | 253 | 248 | 251 | 238 |
IS1663 | 19 | 19 | 21 | 23 | 18 | 20 | 19 | 17 |
IS1002 | 8 | 5 | 8 | 8 | 8 | 7 | 7 | 6 |
Accession number | CP017402 | CP017403 | CP017404 | CP017405 | RSFF00000000 | CP034182 | CP034101 | NC002929 |
Sequencing Platform | PacBio RSII, Illumina MiSeq | PacBio RSII, Illumina MiSeq | PacBio RSII, Illumina MiSeq | PacBio RSII, Illumina MiSeq | Illumina MiSeq | Ion- Torrent Oxford NanoporeMiniON | Ion- Torrent Oxford NanoporeMiniON | Illumina NextSeq |
Contigs | Complete | Complete | Complete | Complete | 264 | Complete | Complete | Complete |
N50 | Complete | Complete | Complete | Complete | 68,043 | Complete | Complete | Complete |
Coverage (x) | 144 | 226 | 239 | 229 | 100 | 203 | 195 | – |
Reference | 42 | 42 | 42 | 42 | 42 | 44 | 44 | 33 |