Table 4 Genomic variants in holarctica isolates with respect to their reference genomes called with three different short-read sequencing datasets
Isolate | FSC237 | 08 T013 | 12 T0050 | 12 T0052 | 12 T0058 | |
|---|---|---|---|---|---|---|
NCBI ID | NC_006570.2 | NC_017463.1 | NC_009749.1 | NC_009749.1 | NC_019551.1 | |
HiSeq | Average coverage | 3910x | 4793x | 1432x | 3232x | 7711x |
SNPs | 0 | 207 | 35 | 35 | 96 | |
Indels | 0 | 2 | 0 | 0 | 0 | |
Miseq | Average coverage | 140x | 102x | 79x | 78x | 89x |
SNPs | 81 | 312 | 153 | 173 | 246 | |
Indels | 0 | 67 | 9 | 12 | 11 | |
Ion Torrent | Average coverage | 185x | 204x | 202x | 163x | 92x |
SNPs | 0 | 189 | 49 | 47 | 94 | |
Indels | 1 | 619 | 611 | 617 | 924 |