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. 2018 Jan 25;34(12):1986–1995. doi: 10.1093/bioinformatics/bty037

Table 2.

Comparison of HPViewer and other programs on detection and genotyping of HPV in recurrent respiratory papillomatosis

Sample ID HPV type: number of reads detected
Bowtie2 with complete HPViewer HPVDetector VirusTAP Vipie
HPV genomes
3T

  • HPV6: 2851

  • HPV71: 1

 HPV6: 2721 HPV6: 2150 HPV6 HPV6
7T

  • HPV6: 386

  • HPV71: 1

 HPV6: 361

  • HPV6: 260

  • HPV11: 2

  • HPV19: 1

  • HPV71: 1

 No hits HPV6
8T HPV6: 1250 HPV6: 1194

  • HPV6: 929

  • HPV71: 1

 HPV6 HPV6
9T HPV11: 4514 HPV11: 4229

  • HPV11: 3481

  • HPV71: 5

 HPV11 HPV11
12T

  • HPV11: 243

  • HPV71: 1

 HPV11: 228

  • HPV11: 167

  • HPV82: 3

 No hits HPV11
15T HPV6: 1285 HPV6: 1223

  • HPV6: 954

  • HPV71: 1

  • HPV82: 1

 HPV6 HPV6
3W

  • HPV6: 2

  • HPV51: 6

  • HPV11: 1

  • HPV71: 7

  • HPV6: 2

  • HPV51: 6

  • HPV6: 1

  • HPV51: 5

  • HPV71: 7

  • HPV82: 2

 No hits No hits
7W

  • HPV6: 2

  • HPV71: 11

  • HPV82: 1

 HPV6: 2

  • HPV19: 1

  • HPV71: 3

  • HPV82: 2

 No hits No hits
8W

  • HPV19: 1

  • HPV71: 2

 No hits

  • HPV19: 2

  • HPV71: 3

 No hits No hits
9W

  • HPV71: 13

  • HPV82: 2

  • HPV20: 1

 No hits

  • HPV71: 3

  • HPV82: 5

 No hits No hits
12W

  • HPV71: 8

  • HPV82: 1

 No hits

  • HPV71: 2

  • HPV82: 4

 No hits No hits
15W

  • HPV71: 19

  • HPV82: 3

 No hits

  • HPV19: 1

  • HPV71: 5

  • HPV82: 1

 No hits No hits

Note: True positive and true negative results are in bold, and false positive results in italic and false negative results in underline.