Table 1. Detected SNPs in HA gene fragment from sample #VIROAF1 (“AF1_HA.csv”).
| # | Sample ID | Sample Name | Chr | Position | Score | Variant Type | Call | Frequency | Depth | Filter |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | VIROAF1 | VIROAF1 | H3N2_CY121792_HA.seq | 51 | 13099 | SNP | A->[G/G] | 1 | 426 | LowGQ |
| 2 | VIROAF1 | VIROAF1 | H3N2_CY121792_HA.seq | 72 | 16707 | SNP | C->[T/T] | 1 | 567 | LowGQ |
| 3 | VIROAF1 | VIROAF1 | H3N2_CY121792_HA.seq | 146 | 23020 | SNP | A->[G/G] | 1 | 864 | LowGQ |
| 4 | VIROAF1 | VIROAF1 | H3N2_CY121792_HA.seq | 182 | 23194 | SNP | G->[A/A] | 1 | 872 | LowGQ |
| 5 | VIROAF1 | VIROAF1 | H3N2_CY121792_HA.seq | 191 | 23154 | SNP | C->[T/T] | 1 | 852 | LowGQ |
| 6 | VIROAF1 | VIROAF1 | H3N2_CY121792_HA.seq | 285 | 17047 | SNP | C->[T/T] | 1 | 620 | LowGQ |
| 7 | VIROAF1 | VIROAF1 | H3N2_CY121792_HA.seq | 308 | 16337 | SNP | T->[A/A] | 1 | 580 | LowGQ |
| 8 | VIROAF1 | VIROAF1 | H3N2_CY121792_HA.seq | 405 | 21306 | SNP | A->[G/G] | 1 | 791 | LowGQ |
| 9 | VIROAF1 | VIROAF1 | H3N2_CY121792_HA.seq | 413 | 20528 | SNP | G->[A/A] | 1 | 760 | LowGQ |
| 10 | VIROAF1 | VIROAF1 | H3N2_CY121792_HA.seq | 456 | 20446 | SNP | C->[T/T] | 1 | 768 | LowGQ |
Each line describes the SNPs at each position in the HA gene fragment of VIROAF1. For instance, position 51 of the HA gene in VIROAF1 is G while the reference allele is A.