Table 2. Next generation sequencing data (Illumina HiSeq 100 base pair fragments) from cassava plants showing Cassava Brown Streak Disease symptoms collected in Kenya in 2013.
| Sample ID | Accession number | Virus | No. of reads obtained | No. of reads after trimming | Number of contigs produced (CLC) | Contig number of positive CBSV/UCBSV and length of postive contig (CLC) | Average coverage (CLCGW) | Number of reads mapped to contig of interest | Ref seq. used for mapping | Length of consensus sequence from mapping (Geneious) |
No. reads mapped to ref. sequence | Average coverage (Geneious) | Final sequence length |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| K1 | MG387659 | CBSV | 15,839,232 | 12,846,217 | 790 | 11 (6081), 12 (2766) | 54,17 | 637, 93 | KR108828 | 8,876 | 4,808 | 55 | 8,748 |
| K2 | MG387657 | CBSV | 18,638,554 | 13,569,714 | 3,117 | 629 (1942), 893 (1931), 285 (1527), 909 (961),1095 (606) | 31,16,34,21,18 | 638, 328, 543, 208, 121 | KR108828 | 8,979 | 2,626 | 30 | 8,745 |
| K4 | MG387653 | UCBSV | 22,774,184 | 17,035,094 | 3,466 | 241(4677), 331(1822), 390(555), 883(1010) | 53,102,32,40 | 34837, 212, 2703, 11742 | FN433933 | 9,437 | 10,495 | 17 | 8,703 |
| K5 | MG387654 | UCBSV | 22,191,388 | 18,507,658 | 766 | 69(4523), 108(1568), 222(574), 452(628), 481(656) | 42,49,18,37,26 | 1908, 770, 105, 247, 173 | FN433933 | 8,824 | 2,174 | 25 | 8,703 |
| K12 | MG387655 | UCBSV | 19,691,178 | 13,917,214 | 884 | 215(2630), 288(2621), 301(2218), 653(780) | 64,34,230,252 | 1717, 1035, 8041, 3483 | FN433933 | 8992 | 2,349 | 27 | 8,614 |
| K13 | MG387652 | UCBSV | 21,979,350 | 15,966,663 | 426 | 148 (562), 222(668), 422(687), 185(733) | 18,11,7,8 | 105, 73, 48, 61 | KR108828 | 8713 | 602 | 7 | 8,703 |
| K14 | MG387656 | UCBSV | 22,543,084 | 16,565,329 | 900 | 18(907), 24(4776), 66(635), 82(1673) | 88,169,118,111 | 816, 8216, 776, 2103 | FN433933 | 8948 | 8,753 | 46 | 8,822 |