Table 3. Detecting variants, stop codons and deletions using two different sequence analysis platforms.
| Lineage Status | Strain | Year | Detected by LoFreq | Detected by VPhaser | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Total Variants a | Stop Codons | Frameshift | Non-Frameshift | Total Variants a | Stop Codons | Frameshift | Non-Frameshift | |||
| Extinct | 32514 | 1998 | 130 | 0 | 0 | 0 | 148 | 0 | 4 | 0 |
| 31459 | 1998 | 51 | 0 | 0 | 0 | 60 | 1 | 7 | 1 | |
| 36957 | 2000 | 56 | 0 | 0 | 0 | 62 | 1 | 9 | 2 | |
| 43826 | 2001 | 57 | 0 | 0 | 0 | 62 | 0 | 10 | 0 | |
| 44988 | 2002 | 59 | 0 | 0 | 0 | 68 | 1 | 2 | 0 | |
| Circulating | 31987 | 1998 | 5 | 0 | 0 | 0 | 12 | 0 | 10 | 1 |
| 47317 b | 2002 | 56 | 0 | 0 | 0 | 58 | 1 | 7 | 1 | |
| 47662 | 2002 | 3 | 0 | 0 | 0 | 4 | 0 | 0 | 0 | |
| 49440 | 2002 | 5 | 0 | 0 | 0 | 21 | 0 | 7 | 2 | |
| 62690 | 1995 | 6 | 0 | 0 | 0 | 12 | 0 | 1 | 0 | |
| 68417 | 2007 | 19 | 0 | 0 | 0 | 74 | 0 | 13 | 0 | |
| 80579 | 2008 | 21 | 0 | 0 | 0 | 22 | 0 | 0 | 0 | |
| Control | I. C | - | 15 | 0 | 0 | 0 | 15 | 0 | 0 | 0 |
a The number of bases that are different from the reference genome.
b Genetic diversity of recombinant DENV-1 strain showing in italic.