Table 4. The outputs of SNPer for the eight fragments of the three different IFVs (“summary.csv”).
| samples_table | sp1 | sp2 | sp3 | all | only_sp1 | only_sp2 | only_sp3 | only_sp1_sp2 | only_sp2_sp3 | only_sp3_sp1 |
|---|---|---|---|---|---|---|---|---|---|---|
| AF1_HA_vs_AF2_HA_vs_AF6_HA | 27 | 22 | 29 | 12 | 6 | 10 | 8 | 0 | 0 | 9 |
| AF1_M_vs_AF2_M_vs_AF6_M | 8 | 6 | 7 | 4 | 1 | 2 | 0 | 0 | 0 | 3 |
| AF1_NA_vs_AF2_NA_vs_AF6_NA | 13 | 12 | 16 | 5 | 3 | 6 | 5 | 0 | 1 | 5 |
| AF1_NEP_vs_AF2_NEP_vs_AF6_NEP | 5 | 4 | 5 | 2 | 0 | 2 | 0 | 0 | 0 | 3 |
| AF1_NP_vs_AF2_NP_vs_AF6_NP | 11 | 9 | 10 | 3 | 3 | 6 | 2 | 0 | 0 | 5 |
| AF1_PA_vs_AF2_PA_vs_AF6_PA | 15 | 8 | 18 | 3 | 3 | 5 | 6 | 0 | 0 | 9 |
| AF1_PB1_vs_AF2_PB1_vs_AF6_PB1 | 18 | 21 | 21 | 9 | 3 | 11 | 5 | 0 | 1 | 6 |
| AF1_PB2_vs_AF2_PB2_vs_AF6_PB2 | 31 | 16 | 26 | 11 | 7 | 5 | 2 | 0 | 0 | 13 |
Each row shows the number of SNPs of VIROAF1 (sp1), VIROAF2 (sp2) and VIROAF6 (sp3) for each fragment after comparison by SNPer. For example, in the first row, the HA fragment contains 27 SNPs in VIROAF1, 22 SNPs in VIROAF2 and 29 SNPs in VIROAF6. Twelve universal SNPs are in VIROAF1, VIROAF2, and VIROAF6. There are six SNPs in only VIROAF1, 10 SNPs in only VIROAF2 and eight SNPs in only VIROAF6. Only nine SNPs exist in both VIROAF6 and VIROAF1.(1)