Table 2 Detection of heterogeneity of type I/II variants in seed and commercial lots of M. bovis BCG Tokyo.

From: Deep sequencing analysis of the heterogeneity of seed and commercial lots of the bacillus Calmette-Guérin (BCG) tuberculosis vaccine substrain Tokyo-172

Position* (gene)

BCG Tokyo

Frequency of nucleotide variants (=Type II) estimated by each package†

1A-825-43

I

II

Tokyo-172

Tokyo-172-1

K-1242-F

KH130

K1478L

BG039304

253,186 (pckA)

A

G

Breseq 35.8/35.7

16.5/17.5

n.d./n.d.

2.4/4.4

13.0/9.0

40.5/39.1

100/100

   

LoFreq 35.1/35.6

16/17.9

n.d./n.d.

2.4/4.6

12.4/8.8

40.0/39.1

100/100

SNVer 36.8/36.4

17.3/17.9

n.d./n.d.

n.d./4.6

13.5/9.0

41.2/40.0

100/100

644,562 (JTY_0567)

T

C

Breseq 35.6/n.d§

19.0/n.d.

n.d./n.d.

2.6/3.4

9.4/9.6

40.0/n.d.

100/100

   

LoFreq 32.8/34.8

17.3/17.0

n.d./n.d.

2.4/3.3

9.3/9.3

38.3/47.2

99.8/99.6

SNVer 35.0/36.1

18.3/18.0

n.d./n.d.

2.5/3.7

10.1/9.3

40.9/48.5

99.8/99.6

765,342 (rpoC)

C

T

Breseq 42.2/33.3

16.7/18.8

n.d./n.d.

2.7/n.d.

10.8/11.7

40.4/40.9

100/100

   

LoFreq 40.5/34.4

15.2/19.1

n.d./n.d.

2.6/3.5

10.8/11.3

39.0/41.2

99.7/99.6

SNVer 43.8/35.0

18.0/19.1

n.d./n.d.

n.d./n.d.

11.9/11.6

41.8/42.0

99.7/99.6

2,717,585 (intergenic†)

C

T

Breseq 40.0/38.5

18.0/20.9

1.4/n.d.

7.2/6.8

10.9/12.4

43.2/47.7

100/100

   

LoFreq 39.3/38.5

16.6/21.4

n.d./n.d.

6.8/6.6

10.4/12.4

41.9/47.7

100/99.8

SNVer 41.9/39.8

19.0/22.5

n.d./n.d.

7.0/6.8

11.3/12.8

44.7/48.5

100/99.8

3,192,638 (ppsA)

.

A

Breseq 34.3/35.2

17.1/19.8

n.d./n.d.

4.3/2.9

10.2/9.8

38.1/45.3

100/n.d.

   

LoFreq –

–

–

–

–

–

–

SNVer 23.7/47.2

n.d./15.3

n.d./n.d.

n.d./n.d.

n.d./8.6

26.4/29.3

46.6/47.2

3,606,131 (JTY_3278)

G

A

Breseq n.d./40.6

n.d./19.6

n.d./n.d.

4.7/5.0

n.d./10.2

n.d./n.d.

100/100

   

LoFreq 43.2/39.9

22.5/19.2

3.1/n.d.

4.7/4.6

12.1/10.1

37.3/41.6

100/100

SNVer 44.9/41.4

23.7/20.1

n.d./n.d.

5.1/n.d.

13.1/10.4

39.1/43.3

100/100

4,087,391 (JTY_3735)

C

T

Breseq 38.8/39.1

17.1/18.3

n.d./n.d.

3.4/3.3

9.0/13.8

43.0/42.7

100/100

   

LoFreq 38.8/40.2

17.0/18.8

n.d./n.d.

3.3/3.7

9.0/14.2

42.3/43.8

100/99.7

SNVer 39.7/40.9

17.5/19.5

n.d./n.d.

3.5/3.7

9.9/14.7

43.9/44.6

100/99.7

  1. *Correspondent to nucleotide positions of genome sequence of M. bovis BCG Tokyo Type I (Accesion No. NC012207).
  2. †Two frequency scores estimated from two read data of each BCG lot are tandemly indicated respectively.
  3. §n.d. not detected.
  4. ‡Left gene: clpX, right gene: mmuM.
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