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Table 1 Validation sample changes

From: Assessment of clinical analytical sensitivity and specificity of next-generation sequencing for detection of simple and complex mutations

Gene

Reference

Change

Coverage

Phred-like confidence Score

% WT

% Mut

A%

C%

G%

T%

Ins%

Del%

ACADVL

NM_000018.2

c.-63_-49dupGGGCGTGCAGGACGC

          
  

c.1375_1376insC

10663

31.5

NA

32

    

31.93

 
  

c.1504C > G (p.L502V)

9193

31

60

38

1.5

58.57

37.59

2.3

0.00

0.04

  

c.1605 + 6 T > C

5733

19.7

68

28

1.71

28.14

2.62

67.54

0.00

0.00

BCKDHA_1

NM_000709.3

c.118dupC

21692

29.5

NA

19

    

19.21

 
  

c.370C > T (p.R124W)

18217

32.3

58

39

1.77

58.36

0.48

39.35

0.00

0.04

BCKDHA_2

NM_000709.3

c.972C > T (p.F324)

15574

30.7

6

91

1.44

5.91

1.36

91.29

0.00

0.01

  

c.995 + 26C > T

18624

33.7

57

41

0.61

57.17

0.85

41.36

0.03

0.02

  

c.995 + 49 G > A

23230

30.3

6

92

91.90

1.10

6.00

0.96

0.00

0.04

  

c.996-33dupC

15037

30.8

NA

75

    

74.61

 

CBS

NM_000071.2

c.959 T > C (p.V320A)

8715

24.4

7

91

0.48

90.82

1.63

7.05

0.00

0.02

  

c.1080C > T (p.A360)

5125

27.3

53

46

0.76

52.55

0.62

46.07

0.00

0.00

CFTR

NM_000492.3

c.1408 G > A (p.M470V)

9356

30.4

60

38

38.44

0.46

60.04

0.99

0.00

0.07

  

c.1521_1523delCTT

5843

22.3

NA

19

0.21

80.35

0.22

0.21

0

19.01

  

c.2052_2053insA

7714

24

NA

26

    

25.68

 

DMD

NM_004006.2

c.2645A > G (p.D882G)

2974

19.6

5

93

4.98

0.87

92.67

1.48

0

0

  

c.5234 G > A (p.R1745H)

4289

23.4

4

93

93.38

1.19

4.13

1.31

0

0

  

c.5326-22 G > T

162

9.6

3

91

3.7

1.85

3.09

91.36

0

0

  

c.6290 + 27 T > A

4085

22.9

3

94

94.15

1.35

1.98

2.5

0

0.02

  

c.8810 G > A (p.R2937Q)

3235

20.1

4

94

94.03

1.08

4.33

0.56

0

0

GAA

NM_000152.3

c.324 T > C (p.C108)

7078

24.7

5

87

4.46

86.61

3.45

5.47

0.00

0.01

  

c.547-4C > G

15200

13.2

5

84

2.89

4.70

84.39

7.99

0.00

0.02

  

c.596A > G (p.H199R)

11616

29.2

9

86

9.13

2.95

85.73

2.18

0.00

0.02

  

c.668 G > A (p.R223H)

10344

31.4

5

93

92.62

1.14

4.89

1.31

0.00

0.04

  

c.858 + 7_858 + 8insAGCGGGC

6175

 

NA

3

    

3

 
  

c.858 + 30 T > C

3431

24.8

5

90

1.40

90.38

2.97

5.25

0.00

0.00

  

c.859-48 T > C

          
  

c.955 + 12 G > A

11315

23.4

4

90

89.60

3.64

3.84

2.90

0.00

0.02

  

c.1203 G > A (p.Q401)

8487

26.1

8

79

79.42

5.35

8.27

6.96

0.00

0.00

  

c.1327-18A > G

7377

26.7

9

82

8.70

5.29

81.81

4.19

0.00

0.01

  

c.1438-19 G > C

2511

16.9

12

75

6.49

75.07

11.59

6.85

0.00

0.00

  

c.1551 + 49C > A

18394

27.9

7

90

89.74

6.59

1.92

1.73

0.00

0.01

  

c.1581 G > A (p.R527)

8283

26.9

70

28

28.05

1.05

70.14

0.76

0.01

0.00

  

c.1802C > T (p.S601L)

6027

21.4

59

34

2.17

59.25

4.35

34.23

0.00

0.00

  

c.1888 + 21 G > A

7667

30.3

56

42

41.99

0.93

56.15

0.94

0.00

0.00

  

c.2040 + 20A > G

5633

27.8

7

91

6.57

1.67

90.96

0.80

0.00

0.00

  

c.2133A > G (p.T711)

8402

29.4

60

39

60.05

0.39

39.20

0.35

0.00

0.01

  

c.2331 + 20 G > A

11993

23

4

92

91.80

2.13

3.91

2.13

0.00

0.03

  

c.2338 G > A (p.V780I)

8957

10.2

11

83

82.93

3.74

10.73

2.57

0.00

0.03

  

c.2553 G > A (p.G851)

11663

21.7

5

94

93.78

0.90

4.54

0.77

0.00

0.00

GALC_1

NM_000153.2

c.328 + 19 T > A

107

0

66

34

33.64

0.00

0.00

66.36

0.00

0.00

  

c.329-35 G > A

          
  

c.550C > T (p.R184C)

9215

19.6

39

54

2.59

38.77

4.75

53.88

0

0

  

c.621 + 24 T > C

1178

17.1

82

16

1.61

15.87

0.34

82.17

0

0

  

c.742 G > A (p.D248N)

15664

32.8

62

35

35.28

0.5

61.78

2.43

0

0.01

  

c.1161 + 38 T > C

5842

29.6

56

42

0.77

42.23

0.74

56.23

0

0.03

  

c.1586C > T (p.T529M)

15938

25.7

16

78

2.41

16.18

3.38

78.02

0

0.01

  

c.1620A > G (p.T540)

25811

31.3

3

95

3.42

1.12

94.6

0.85

0

0.02

  

c.1671-15C > T

17257

21.1

5

93

1.17

4.9

1.05

92.86

0

0.01

  

c.1698A > T (p.V566)

41239

26.7

2

96

2.16

1.04

0.65

96.13

0

0.03

  

c.1834 + 5C > G

10158

18.2

84

15

0.21

84.13

15.16

0.41

0.01

0.09

  

c.1921A > G (p.T641A)

20556

23.6

2

97

2.13

0.88

96.5

0.49

0

0.01

GALC_2

NM_000153.2

c.328 + 19 T > A

193

0

85

15

15.03

0.00

0.00

84.97

0.00

0.00

  

c.984 G > A (p.Q328)

17041

27.1

61

37

37

1.38

60.55

1.06

0

0

  

c.1350C > T (p.S450)

17776

32.2

58

40

1.04

57.78

1.6

39.58

0

0.01

  

c.1620A > G (p.T540)

25799

31.6

3

95

3.21

1.05

94.97

0.76

0

0.01

  

c.1671-15C > T

22892

32.8

64

34

0.87

63.97

0.7

34.45

0

0.02

  

c.1685 T > C (p.I562T)

30664

31.2

58

39

1.99

38.95

1.47

57.58

0

0.01

  

c.1698A > T (p.V566)

42340

29.3

2

96

1.97

1.11

0.63

96.24

0

0.05

  

c.1834 + 5C > G

10344

13.1

73

26

0.26

73.18

25.98

0.55

0

0.03

  

c.1921A > G (p.T641A)

15648

23

2

96

2.19

1.04

96.42

0.35

0

0.01

GALT

NM_000155.2

c.776 G > A (p.R259Q)

27403

31.3

62

32

31.51

2.92

62.00

3.55

0.05

0.02

  

c.817 G > C (p.D273H)

27824

32.3

61

38

0.68

37.71

60.85

0.73

0.00

0.03

GBA_1

NM_001005741.2

c.1225-34C > A

2621

22.8

2

96

96.26

2.21

1.14

0.38

0

0

  

c.1226 A > G (p.N409S)

2864

20.4

62

36

61.91

0.8

36.03

1.26

0

0

  

c.1448 T > C (p.L483P)

3331

26.4

60

38

0.99

38.04

0.9

60.07

0

0

  

c.1483 G > C (p.A495P)

2569

16.3

53

44

1.01

44.45

53.41

1.05

0

0.08

  

c.1497 G > C (p.V499)

2750

22.2

60

37

1.16

36.69

59.71

2.44

0

0

GBA_2

NM_001005741.2

IVS8-34C > A

2827

22

3

96

96.11

2.51

1.13

0.25

0

0

  

c.1226 A > G (p.N409S)

3813

22.9

71

23

70.52

1.1

26.86

1.52

0

0

  

c.1265-1317 del55

20

26.9

NA

25

     

25

GJB2

NM_004004.5

c.35dupG

33377

20.8

NA

18

0.74

0.33

1.28

96.64

17.63

1.01

  

c.35delG

34879

29.7

NA

30

     

29.71

HEXB

NM_000521.3

c.185 T > C (p.L62S)

21320

33.2

8

86

3.63

86.44

2.33

7.59

0.00

0.02

  

c.362A > G (p.K121R)

14201

27.9

66

32

65.63

1.11

31.86

1.39

0.00

0.00

  

c.300-32C > T

792

20.5

80

17

1.77

80.05

1.26

16.92

0.00

0.00

  

c.558 + 45 G > A

434

18.8

81

17

17.05

1.15

80.65

1.15

0.00

0.00

  

c.1513C > T (p.R505W)

8306

30.9

62

37

0.52

61.77

0.92

36.78

0.00

0.01

  

c.1619_1620ins22

27194

 

NA

67

      
  

c.1645 G > A (p.G549R)

33259

34.6

84

15

15.46

0.47

83.69

0.36

0.00

0.02

IDUA

NM_000203.3

c.99 T > G / p.H33Q

34

10.2

6

91

2.94

0.00

91.18

5.88

0.00

0.00

  

c.208C > T (p.Q70X)

4106

9.4

49

46

2.65

49.05

1.90

46.40

0.00

0.00

  

c.300-44C > T

10156

26.2

59

40

0.74

58.71

0.96

39.55

0.00

0.03

  

c.314 G > A (p.R105Q)

10809

28.7

62

34

33.71

1.86

62.39

2.01

0.00

0.03

  

c.543 T > C (p.N181)

12274

31.7

59

39

1.52

38.63

0.91

58.91

0.00

0.02

  

c.590-45 G > C

11498

28.5

63

35

1.10

35.31

62.92

0.67

0.00

0.01

  

c.590-8C > T

9516

30.8

63

34

1.46

63.36

1.04

34.03

0.00

0.12

  

c.942 G > C (p.A314)

6026

20.9

63

34

2.09

29.67

66.69

1.51

0.00

0.03

  

c.972 + 48A > G

1954

25.2

67

30

82.96

0.82

15.81

0.36

0.00

0.05

  

c.973-45 G > C

          
  

c.1081 G > A (p.A361T)

9486

26.7

60

38

37.50

1.18

59.99

1.33

0.00

0.00

  

c.1164 G > C (p.T388T)

3080

23.1

65

31

2.05

31.30

65.16

1.49

0.00

0.00

  

c.1205 G > A (p.W402X)

2679

23.2

62

32

31.88

5.30

61.55

1.27

0.00

0.00

OPA1

NM_015560.2

c.93_96dupAAAA

179

0

NA

69

    

69.27

 
  

c.870 + 4 T > C

8330

28.8

3

97

2.23

89.09

1.81

6.87

0.00

0.00

  

c.2808 G > A (p.A936)

8879

23

66

28

27.91

2.87

65.95

3.23

0.00

0.03

RECQL4

NM_004260.2

c.132A > G (p.E44)

5504

28.7

61

37

60.74

1.58

37.08

0.58

0

0.02

  

c.274 T > C (p.S92P)

2505

11.9

14

75

4.79

74.61

6.43

14.17

0

0

  

c.738C > T (p.S246S)

10356

27.9

76

24

0.3

75.69

0.32

23.68

0

0.02

  

c.801 G > C (p.E267D)

5788

28.6

64

34

0.57

34.45

63.99

0.93

0

0.05

  

c.1258 + 18 G > A

11609

27

65

31

30.65

2.64

64.82

1.86

0

0.03

  

c.1621-15C > T

2331

26.6

63

34

1.12

63.32

1.54

34.02

0

0

  

c.2297delC

8864

25

NA

94

0.37

3.77

1.55

0.17

0.01

94.14

  

c.3014 G > A (p.R1005Q)

3027

27

50

48

47.9

1.06

50.21

0.83

0

0

  

c.3127 T > C (p.L1043L)

13424

30.6

5

94

0.77

93.66

0.99

4.53

0

0.04

  

c.3236 + 13C > T

1938

12

66

30

2.06

66.25

1.65

30.03

0

0

  

c.3393 + 8C > T

2898

24.4

61

36

1.69

61.15

1.38

35.78

0

0

  

c.3502 + 24 G > A

1106

20.2

64

30

29.57

2.35

64.2

3.8

0

0.09

SGSH

NM_000199.3

c.337_345delins11

7735

27.4

NA

23

     

22.82

  

c.663 + 17 T > C

11973

29.6

59

39

0.93

38.84

1.24

58.96

0

0.04

  

c.664-39_664-38delCT

153

30.6

NA

18

0

0

0

82.35

0

17.65

  

c.664-36 T > C

149

30.5

82

18

0.00

18.12

0.00

81.88

0.00

0.00

  

c.892 T > C (p.S298P)

12564

31.7

60

38

0.93

37.61

1.13

60.31

0

0.02

  

c.1367 G > A (p.R456H)

8525

29.5

61

36

36.29

1.69

60.75

1.23

0

0.04

SMPD1

NM_000543.4

c.103CTGGCG[7]

5073

22.2

NA

88

     

88.07

  

c.107 T > C (p.V36A)

          
  

c.785_807del23

10467

22.1

NA

20

0.06

0.16

0.01

79.68

0.01

20.09

ZEB2

NM_014795.3

c.2083C > T (p.R695X)

20800

24.9

75

24

0.51

75.22

0.4

23.88

0

0

  

c.3067 + 6A > T

2632

24.3

60

39

59.95

0.68

0.53

38.79

0

0.04

  1. Changes being assayed for in the 20 validation samples, along with corresponding coverage and reference sequence used during data analysis.
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