Table 3 Main features of Illumina MiSeq sequencing Run obtained after Trimmomatic, SPADES and SAMtools application
Total reads | Total reads after Trimmomatic | Total reads after SPADES | Number of reads aligned | |
|---|---|---|---|---|
1 (BL) | 5,470,168 | 5,220,204 | 5,219,176 | NS3 88,766 |
NS5A 2,952,378 | ||||
NS5B 1,722,432 | ||||
1 (FA) | 839,254 | 622,494 | 619,064 | NS3 30,329 |
NS5A 232,894 | ||||
NS5B 273,387 | ||||
2 (BL) | 4,422,614 | 4,248,300 | 4,207,974 | NS3 2,184,866 |
NS5A 1,476,874 | ||||
NS5B 136,248 | ||||
2 (FA) | 3,956,108 | 3,726,938 | 3,677,042 | NS3 455,654 |
NS5A 1584.345 | ||||
NS5B 1,251,540 | ||||
3 (BL) | 3,956,876 | 3,611,990 | 3,535,350 | NS3 244,237 |
NS5A 649,235 | ||||
NS5B 1,746,295 | ||||
3 (FA) | 3,910,498 | 3,669,880 | 3,607,316 | NS3 80,326 |
NS5A 166,688 | ||||
NS5B 3,136,304 | ||||
4 (BL) | 3,830,412 | 3,636,298 | 3,591,446 | NS3 30,775 |
NS5A 1,416,729 | ||||
NS5B 1,925,610 | ||||
4 (FA) | 3,745,704 | 3,590,586 | 3,555,526 | NS3 112,212 |
NS5A 1,284,284 | ||||
NS5B 1,967,277 |