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. 2013 Feb 19;14:6. doi: 10.1186/1471-2156-14-6

Table 1.

Validation sample changes

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

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