Supplementary Table 1 Average Depth of Coverage

Supplementary Table 1: Average Depth of Coverage Mean  % Target Bases  % Target  % Target  % Target  % Target  % Reads  % Reads  Median  Target  with Zero  Bases with 2x  Bases with  Bases with  Bases with  Aligned in  Genome Size  Patient Aligned Insert Size Coverage Coverage Coverage 10x Coverage 20x Coverage 30x Coverage Pairs (bp) BRE‐0109 0.95 121 181.72 0.01 0.85 0.81 0.75 0.69 0.99 3101804739 BRE‐1095 0.96 103 386.85 0.00 0.95 0.89 0.85 0.80 0.99 3101804739 BRE‐0113 0.94 138 186.78 0.00 0.94 0.85 0.78 0.72 0.99 3101804739 BRE‐1150 0.98 159 332.9 0.00 0.96 0.94 0.91 0.89 1.00 3101804739 BRE‐0128 0.95 122 224.19 0.01 0.89 0.85 0.80 0.75 0.99 3101804739 BRE‐0015 0.97 121 229.93 0.01 0.91 0.86 0.80 0.76 0.99 3101804739 BRE‐0150 0.97 106 430.63 0.00 0.96 0.90 0.86 0.82 0.99 3101804739 BRE‐0174 0.97 127 233.03 0.00 0.89 0.85 0.79 0.74 0.99 3101804739 BRE‐0178 0.71 94 74.71 0.02 0.79 0.65 0.54 0.46 0.98 3101804739 BRE‐0179 0.99 162 1053.62 0.00 0.97 0.96 0.95 0.94 1.00 3101804739 BRE‐0018 0.96 114 476.55 0.00 0.92 0.89 0.86 0.83 0.99 3101804739 BRE‐0184 0.98 145 335.85 0.00 0.95 0.92 0.89 0.86 1.00 3101804739 BRE‐0185 0.99 158 217.05 0.00 0.96 0.93 0.89 0.86 1.00 3101804739 BRE‐0191 0.99 163 290.18 0.00 0.97 0.94 0.91 0.88 1.00 3101804739 BRE‐0193 0.99 148 399.72 0.00 0.97 0.94 0.91 0.89 1.00 3101804739 BRE‐0194 0.97 107 420.19 0.00 0.96 0.92 0.88 0.84 0.99 3101804739 BRE‐0196 0.98 162 373.2 0.00 0.96 0.95 0.92 0.90 1.00 3101804739 BRE‐0198 0.82 71 64.28 0.04 0.66 0.47 0.36 0.30 0.99 3101804739 BRE‐0200 0.98 114 358.96 0.00 0.96 0.91 0.87 0.83 0.99 3101804739 BRE‐0202 0.98 111 492.06 0.00 0.97 0.93 0.89 0.86 0.99 3101804739 BRE‐0203 0.97 112 439.26 0.00 0.96 0.92 0.89 0.85 0.99 3101804739 BRE‐0205 0.99 164 238.55 0.00 0.96 0.93 0.89 0.85 1.00 3101804739 BRE‐0021 0.96 131 265.97 0.00 0.89 0.85 0.81 0.77 0.99 3101804739 BRE‐0210 0.92 112 101.35 0.02 0.78 0.72 0.64 0.58 0.99 3101804739 BRE‐0211 0.99 168 201.52 0.00 0.97 0.93 0.90 0.87 1.00 3101804739 BRE‐0217 0.96 111 273.34 0.00 0.95 0.89 0.84 0.79 0.99 3101804739 BRE‐0218 0.95 105 247.69 0.00 0.93 0.84 0.76 0.70 0.99 3101804739

GC% 0.51 0.5 0.48 0.49 0.51 0.51 0.52 0.52 0.52 0.5 0.53 0.5 0.5 0.5 0.51 0.52 0.49 0.54 0.53 0.52 0.52 0.52 0.51 0.51 0.5 0.51 0.54

BRE‐0223 BRE‐0225 BRE‐0229 BRE‐0023 BRE‐0233 BRE‐0235 BRE‐0266 BRE‐0274 BRE‐0296 BRE‐0317 BRE‐0324 BRE‐0327 BRE‐0331 BRE‐0332 BRE‐0333 BRE‐0336 BRE‐0340 BRE‐0346 BRE‐0358 BRE‐0360 BRE‐0371 BRE‐0372 BRE‐0375 BRE‐0380 BRE‐0386 BRE‐0389 BRE‐0391 BRE‐0396 BRE‐0406 BRE‐0407 BRE‐0409 BRE‐0413 BRE‐0416

0.91 0.98 0.84 0.99 0.95 0.96 0.97 0.85 0.98 0.96 0.97 0.98 0.96 0.95 0.97 0.98 0.98 0.78 0.99 0.94 0.97 0.91 0.94 0.90 0.98 0.99 0.98 0.97 0.97 0.93 0.97 0.99 0.96

90 148 85 163 108 104 105 78 136 130 130 145 124 118 101 122 141 71 157 100 106 90 94 97 141 167 143 131 137 116 124 175 100

222 1706.9 104.34 346.05 311.56 342.93 321.66 107.72 369.84 120.23 160.47 238.65 114.26 141.51 449.67 223.37 188.4 58.26 266.67 262.91 469.89 123.39 269.74 126.55 165.24 771.91 448.49 159.66 338.06 79.86 226.87 263.73 269.28

0.01 0.00 0.01 0.00 0.00 0.00 0.00 0.02 0.00 0.01 0.00 0.00 0.01 0.01 0.00 0.00 0.00 0.03 0.00 0.00 0.00 0.01 0.01 0.03 0.00 0.00 0.00 0.00 0.00 0.02 0.00 0.00 0.00

0.86 0.96 0.81 0.97 0.95 0.95 0.95 0.76 0.95 0.89 0.92 0.95 0.89 0.85 0.95 0.93 0.96 0.70 0.96 0.92 0.96 0.82 0.87 0.73 0.94 0.98 0.96 0.93 0.94 0.82 0.92 0.97 0.94

0.74 0.95 0.67 0.95 0.89 0.89 0.88 0.63 0.91 0.83 0.86 0.90 0.81 0.80 0.89 0.89 0.92 0.52 0.94 0.84 0.92 0.66 0.77 0.65 0.89 0.96 0.94 0.87 0.92 0.74 0.88 0.94 0.87

0.66 0.95 0.57 0.92 0.84 0.84 0.83 0.53 0.88 0.76 0.81 0.86 0.73 0.73 0.84 0.85 0.88 0.40 0.91 0.78 0.90 0.55 0.69 0.57 0.84 0.95 0.92 0.82 0.89 0.64 0.84 0.91 0.81

0.60 0.94 0.50 0.90 0.80 0.80 0.78 0.46 0.85 0.69 0.76 0.82 0.66 0.67 0.80 0.81 0.84 0.32 0.88 0.72 0.87 0.48 0.64 0.51 0.79 0.94 0.89 0.77 0.86 0.57 0.81 0.89 0.76

0.99 1.00 0.99 1.00 0.99 0.99 0.99 0.99 1.00 0.99 1.00 1.00 0.99 0.99 0.99 1.00 1.00 0.98 1.00 0.99 0.99 0.99 0.99 0.99 1.00 1.00 1.00 1.00 1.00 0.99 1.00 1.00 0.99

3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739

0.53 0.53 0.53 0.5 0.51 0.52 0.52 0.52 0.51 0.49 0.51 0.52 0.51 0.51 0.53 0.49 0.48 0.53 0.48 0.52 0.49 0.53 0.54 0.52 0.51 0.49 0.5 0.5 0.48 0.5 0.49 0.5 0.49

BRE‐0423 BRE‐0438 BRE‐0439 BRE‐0440 BRE‐0045 BRE‐0470 BRE‐0478 BRE‐0049 BRE‐0050 BRE‐0053 BRE‐0583 BRE‐0591 BRE‐0596 BRE‐0597 BRE‐0608 BRE‐0614 BRE‐0642 BRE‐0065 BRE‐0656 BRE‐0067 BRE‐0069 BRE‐0073 BRE‐0075 BRE‐0076 BRE‐0773 BRE‐0777 BRE‐0083 BRE‐0097

0.99 0.98 0.98 0.98 0.95 0.95 0.99 0.99 0.76 0.76 0.99 0.98 0.99 0.99 0.95 0.97 0.94 0.98 0.97 0.98 0.97 0.95 0.90 0.95 0.93 0.98 0.90 0.94

162 112 113 109 102 99 164 161 65 65 168 116 174 136 94 100 92 142 102 140 129 130 91 103 89 120 119 100

220.57 310.85 441.21 473.31 298.09 231.81 257.65 260.63 54.5 44.32 368.94 439.29 244.96 517.65 229.12 219.69 192.25 376.1 361.21 439.62 359.77 122.26 159.47 308.43 263.02 636.98 93.22 303.79

0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.06 0.07 0.00 0.00 0.00 0.00 0.00 0.00 0.01 0.00 0.00 0.00 0.01 0.02 0.02 0.01 0.01 0.00 0.03 0.00

0.96 0.96 0.96 0.96 0.93 0.93 0.97 0.97 0.56 0.61 0.97 0.96 0.97 0.91 0.90 0.94 0.89 0.94 0.95 0.94 0.88 0.79 0.78 0.91 0.83 0.97 0.75 0.92

0.92 0.91 0.92 0.92 0.85 0.84 0.94 0.93 0.40 0.41 0.95 0.93 0.94 0.81 0.81 0.86 0.79 0.92 0.91 0.91 0.85 0.58 0.61 0.80 0.75 0.96 0.66 0.83

0.89 0.86 0.88 0.88 0.79 0.78 0.91 0.90 0.30 0.30 0.92 0.90 0.91 0.74 0.73 0.78 0.70 0.90 0.86 0.88 0.81 0.46 0.50 0.71 0.68 0.94 0.58 0.76

0.86 0.82 0.85 0.85 0.73 0.72 0.88 0.87 0.24 0.24 0.91 0.87 0.88 0.69 0.67 0.73 0.64 0.87 0.83 0.85 0.77 0.39 0.43 0.65 0.62 0.92 0.51 0.71

1.00 0.99 1.00 1.00 0.99 0.99 1.00 1.00 0.98 0.98 1.00 0.99 1.00 1.00 0.99 0.99 0.99 1.00 0.99 1.00 1.00 0.99 0.99 0.99 0.99 1.00 0.98 0.99

3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739 3101804739

0.51 0.52 0.53 0.52 0.53 0.5 0.48 0.51 0.55 0.55 0.5 0.5 0.5 0.56 0.52 0.51 0.52 0.5 0.49 0.52 0.53 0.52 0.56 0.56 0.53 0.49 0.51 0.52