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Table 1 Comparison of alignment methods and cFinder to manual approach

From: cFinder: definition and quantification of multiple haplotypes in a mixed sample

Sample (no.)

Clone variants

Manual

cFinder (AVA)

cFinder (CLCbio)

%

Hits

%

Hits

%

Hits

1

c.749 G>A

22.0

14,956

23.3

15,611

22.43

14,745

 

c.757 T>C

26.5

18,458

30.6

20,886

29.39

19,604

2

c.749G>A, c.943A>G, c.1497A>G

15.7

4748

6.4

4362

6.21

4066

 

c.749G>A, c.949T>A, c.1497A>G

4.1

1240

2.4

1641

2.3

1522

 

c.749G>A, c.1497A>G

22.7

6864

7.1*

4145

6.7*

3729

 

c.943A>G, c.1497A>G

17.1

16,237

12.6

9183

12.5

8715

 

c. 949T>A, c.1497A>G

3.3

3128

4.5

3342

4.6

3240

 

c.1497A>G

45.2

26,522

61.2*

35,867*

61.3*

33,804

 

c.749G>A, c.949T>A

–

–

3.4

2519

3.5

2488

 

c.749G>A

–

–

13.9

7996

14.2

8074

 

c.749G>A, c.943A>G

–

–

10.8

7838

10.9

7692

 

c.943A>G

–

–

4.0

3483

4.2

3574

 

c.949T>A

–

–

1.1

991

1.2

1023

3

c.1375G>A, c.1423_1424ins35

6.2

3495

5.9

3186

6.4

3019

 

c.1375G>A

90.9

51,247

90.9

51,891

87.9

42,693*

4

c.730A>G

20.3

9887

27.5

17,769

27.5

17,483*

5

c.756G>T, c.1086_1270del185

5.4

1407

6.2

1406

6.8

1490

 

c.756G>T, c.1423_1424ins35

1.0

160

1.6

244

0.2**

30

 

c.756G>T

41.0

10,845

58.9*

12,446*

57.3*

11,545

 

c.1423_1424ins35

–

–

1.6

244

1.6

235

 

c.1086_1270del185

2.7

727

2.6

625

2.6

611

 

c.888_919del32

1.6

427

0.9**

220

0.2**

40

6

c.756G>>T, c.1086_1270del185

20.4

8151

14.1

7922

14.1

7702

 

c.1086_1270del185

–

–

6.3

4008

4.6

2828

 

c.756G>T

64.6

32,472

65.0

31,932

63.3

30,093

7

c.756G>T

51.2

38,883

62.3*

38,726

61.5*

37,336

8

c.838_1378del540, c.1423_1424ins35

98.4

49,425

–

–

85.7*

47,729

 

c.1423_1424ins35

–

–

–

–

2.1

1187

 

c.838_1378del540

–

–

–

–

10.8

6013

9

c.825G>A

2.2

229

3.1

269

3.0

250

10

c.1086_1270del185, c.1423_1424ins35

1.3

278

0.5**

132

0.5**

116

 

c.944C>T, c.1086_1270del185

9.1

2260

7.5

2215

5.3

1548

 

c.944C>T

30.6

9778

33.7

10,069

34.3

10,061

 

c.1086_1270del185

12.1

3278

10.4

3026

7.4

2164

 

c.1423_1424ins35

2.1

460

1.9

384

1.8

375

  1. Sample and found clone variants are listed with their percentage of occurrence and the hits (absolute number of reads with that variant), comparing manual detection with automated analysis with cFinder with two different alignment software products. Results marked with one star (*) show intense deviation from manual findings, numbers marked with two stars (**) fell below threshold of 1 %. If clone was not detected it is marked with a dash (–)
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BMC Research Notes

ISSN: 1756-0500

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