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.

O'Dushlaine and Shields BMC Genomics 2006 7:290   doi:10.1186/1471-2164-7-290