Table 1. De novo assembly and mapping of viral reads using CLC Genomic Workbench version 8.5.1 and Geneious 8.1.8.
| Sample ID | Virus | Number of reads | Number of reads after trimming | Number of contigs produced | Reference sequence used for mapping | Length of consensus sequence from mapping (Geneious) | Number of reads mapped to reference sequence | Mean coverage (Geneious) | Contig positive for virus and length | Average coverage (CLCGW) | Number of reads mapped to contig of interest | % Similarity BLAST | Final sequence length |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SRF 109a | SPFMV | 12,667,976 | 10,995,262 | 9,269 | FJ155666 | 11,424 | 890,045 | 11944.7 | 5(10,218) | 11,890 | 884,699 | 96 | 10,482 |
| SPVC | KU877879 | 11,410 | 466,349 | 6133.5 | 9(10,368) | 4,309 | 325,619 | 93;95 | 10,392 | ||||
| SPCFV | KU720565 | 10,305 | 280,077 | 4383.5 | 19(8,427) | 5,430 | 335,367 | 97 | 9,414 | ||||
| SPCSV(RNA1)/RNA2 | NC_004123 | 12,610 | 76,902 | 1169.4 | 85(16,157) | 1,339 | 164,959 | 99 | 16,157 |
Note:
The four sweet potato viruses identified were: Sweet potato feathery mottle virus (SPFMV), Sweet potato virus C (SPVC), Sweet potato chlorotic fleck (SPCFV) and Sweet potato chlorotic stunt virus (SPCSV).