Table 2.
Comparisons between VNTRfinder and the method described by Denoeud and Vergnaud.
| Mycobacterium tuberculosis (99.3% identical) | Neisseria meningitidis (48.74% identical) | ||||||||
| Total | % Denoeud aligned TRs aligned by VNTRfinder | % of Denoeud VNTRs called by VNTRfinder as variant or non-variant | % of Denoeud non-variants called by VNTRfinder as variant or non-variant | Total | % Denoeud aligned TRs aligned by VNTRfinder | % of Denoeud VNTRs called by VNTRfinder as variant or non-variant | % of Denoeud non-variants called by VNTRfinder as variant or non-variant | ||
| Denoeud v. 40, 10, all variants | Denoeud v. 40, 10, all variants | ||||||||
| total repeats matched | 10860 | 86.59 | total repeats matched | 3533 | 82.18 | ||||
| DEN+, VNTRfinder+ * | 72 | 94.7 | DEN+, VNTRfinder+ | 69 | 81.2 | ||||
| DEN+, VNTRfinder- | 4 | 5.3 | DEN+, VNTRfinder- | 16 | 18.8 | ||||
| DEN-, VNTRfinder+ | 0 | 0 | DEN-, VNTRfinder+ | 2 | 0 | ||||
| DEN-, VNTRfinder- | 10784 | 100 | DEN-, VNTRfinder- | 3446 | 100 | ||||
| Denoeud v. 40, 10, multiple of unit | Denoeud v. 40, 10, multiple of unit | ||||||||
| total repeats matched | 10160 | 81.01 | total repeats matched | 1615 | 37.57 | ||||
| DEN+, VNTRfinder+ | 39 | 92.9 | DEN+, VNTRfinder+ | 9 | 75.0 | ||||
| DEN+, VNTRfinder- | 3 | 7.1 | DEN+, VNTRfinder- | 3 | 25.0 | ||||
| DEN-, VNTRfinder+ | 0 | 0 | DEN-, VNTRfinder+ | 0 | 0 | ||||
| DEN-, VNTRfinder- | 10118 | 100 | DEN-, VNTRfinder- | 1603 | 100 | ||||
* '+/-' indicate repeats reported as variants/non-variants.
Repeats were matched between the results reported by VNTRfinder and those reported by the method of Denoeud and Vergnaud.