Table 4.
Variable SNP calls discovered with resequencing and results after these were passed through our data filter.
| Position | Description |
|---|---|
| 204781 | Missing after MUSCLE |
| 255578 | Homopolymer (8 T/A) |
| 355131 | Missing after MUSCLE |
| 756435 | Homopolymer (9 C/G) |
| 1070504 | SNP in Gap |
| 1097814 | Homopolymer (9 T/A) |
| 1179704 | Homopolymer (7 T/A) |
| 1205130 | Good (but ambiguous after looking at assembly) |
| 1368882 | Missing after MUSCLE |
| 1642240 | Missing after MUSCLE |
| 1693620 | Homopolymer (6 T/A) |
| 1713322 | Missing after MUSCLE |
| 1806153 | Homopolymer (6 T/A) |
| 2087876 | Missing after MUSCLE |
| 2354057 | Homopolymer (6 T/A) |
| 2545225 | Missing after MUSCLE |
| 3193883 | Homopolymer (7 T/A) |
| 3823524 | Good |
| 4257557 | Homopolymer (8 T/A) |
| 4545198 | SNP in Gap |
| 4545878 | Duplicated in other Salmonella (Elongation Factor Tu) |
| 4546413 | SNP in Gap |
| 4548105 | 23S rRNA |
Details of the variation arising from resequencing are listed including the variable site location, a description of the variant, the nucleotide change and corrections during our rapid data analysis pipeline.