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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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