Fig. 1.
Fig. 2.
Fig. 3.
Fig. 4.
The results of the analysis of the genetic composition of three commercial poultry infectious bronchitis vaccines carried out using the Kraken2 and Burrows–Wheeler Aligner (BWA) tools
| Vaccine | Batch | Number of reads | BWA | Kraken2 | |||
|---|---|---|---|---|---|---|---|
| % of reads mapped to the IBV genome | % of reads mapped to the Gallus gallus genome | % of reads mapped to the avian coronavirus genome | % of reads mapped to eukaryotic genome | % of reads mapped to bacterial genome | |||
| V-01 | 01 | 3,911,175 | 86 | 14 | 73 | 13 | 15 |
| 02 | 3,260,251 | 84 | 16 | 70 | 15 | 14 | |
| 03 | 3,971,161 | 89 | 10 | 75 | 10 | 15 | |
| V-02 | 01 | 4,172,990 | 85 | 14 | 83 | 8 | 9 |
| 02 | 4,487,555 | 84 | 15 | 81 | 8 | 11 | |
| 03 | 5,090,925 | 85 | 14 | 83 | 7 | 10 | |
| V-03 | 01 | 4,712,611 | 68 | 31 | 58 | 23 | 19 |
| 02 | 4,193,830 | 75 | 23 | 63 | 16 | 21 | |
| 03 | 1,181,940 | 51 | 48 | 43 | 39 | 18 | |
The vcf-annotator tool results of viral variant type analyses of commercial poultry infectious bronchitis vaccines sequenced with high throughput
| Vaccine Batch | Total variants | Unique variants | |||||||
|---|---|---|---|---|---|---|---|---|---|
| Total number of variants | Type of changes | Number of unique variants | Type of changes | ||||||
| Synonymous | Non-synonymous | Unknown | Synonymous | Non-synonymous | Unknown | ||||
| V-01 | 01 | 35 | 8 | 22 | 5 | 7 | 2 | 2 | 3 |
| 02 | 38 | 7 | 22 | 9 | 10 | 1 | 2 | 7 | |
| 03 | 35 | 7 | 21 | 7 | 7 | 1 | 1 | 5 | |
| V-02 | 01 | 7 | 1 | 4 | 2 | 0 | 0 | 0 | 0 |
| 02 | 8 | 1 | 4 | 3 | 1 | 0 | 0 | 1 | |
| 03 | 11 | 1 | 4 | 6 | 4 | 0 | 0 | 4 | |
| V-03 | 01 | 3 | 1 | 0 | 2 | 0 | 0 | 0 | 0 |
| 02 | 8 | 0 | 1 | 7 | 5 | 0 | 0 | 5 | |
| 03 | 5 | 0 | 2 | 3 | 2 | 0 | 1 | 1 | |