## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5271-Z0010-CACTGCACGAATGAT/441525-L5271-Z0010-CACTGCACGAATGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5271-Z0010-CACTGCACGAATGAT/441525-L5271-Z0010-CACTGCACGAATGAT_SNVQ.metric USE_ACTUAL_ORIGINAL_QUALITIES=false INCLUDE_SECONDARY_ALIGNMENTS=false INCLUDE_SUPPLEMENTAL_ALIGNMENTS=false ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader # Started on: Fri Mar 13 03:02:05 EDT 2026 ## METRICS CLASS picard.analysis.CollectQualityYieldMetricsSNVQ$QualityYieldMetrics TOTAL_READS PF_READS READ_LENGTH TOTAL_BASES PF_BASES Q20_BASES PF_Q20_BASES Q30_BASES PF_Q30_BASES Q40_BASES PF_Q40_BASES PCT_Q20_BASES PCT_Q30_BASES PCT_Q40_BASES PCT_PF_Q20_BASES PCT_PF_Q30_BASES PCT_PF_Q40_BASES TOTAL_SNVQ PF_SNVQ Q20_SNVQ PF_Q20_SNVQ Q30_SNVQ PF_Q30_SNVQ Q40_SNVQ PF_Q40_SNVQ PCT_Q20_SNVQ PCT_Q30_SNVQ PCT_Q40_SNVQ PCT_PF_Q20_SNVQ PCT_PF_Q30_SNVQ PCT_PF_Q40_SNVQ 1000323 1000323 139 139326975 139326975 134243932 134243932 124625492 124625492 0 0 0.963517 0.894482 0 0.963517 0.894482 0 417980925 417980925 411279194 411279194 395889706 395889706 370017578 370017578 0.983966 0.947148 0.88525 0.983966 0.947148 0.88525 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 959 0 35.993162 40.995152 1 12910 1 35.98658 40.990891 2 15743 5473 35.992866 40.993971 3 39147 1445 35.972694 40.978286 4 62526 54600 35.98817 40.990372 5 124951 19103 35.992236 40.994049 6 116431 142923 35.963943 40.969349 7 215312 177576 35.973864 40.981768 8 198874 162007 35.984892 40.988197 9 255084 122322 35.953281 40.96137 10 265801 541155 35.882971 40.926845 11 309832 70494 35.919713 40.941727 12 360318 741193 35.299649 40.41207 13 355291 217061 33.955718 39.731775 14 478205 1019308 35.878772 40.926009 15 388356 390098 35.795372 40.855002 16 389888 439802 35.747276 40.776816 17 535939 1119325 35.885073 40.902473 18 567864 769212 35.664791 40.720671 19 389612 708633 35.724795 40.787073 20 546654 1012806 35.910228 40.937899 21 694712 1447222 35.826212 40.87485 22 347198 561574 35.575518 40.708726 23 1117943 1316924 35.240819 40.483979 24 612997 1259447 35.217027 40.470321 25 568924 498379 35.22326 40.471595 26 1831640 2675666 35.163997 40.426568 27 381165 931121 35.186016 40.445709 28 992662 425178 35.19954 40.456392 29 2524545 5261171 35.192163 40.450591 30 818754 44449 35.19116 40.447715 31 2439306 904994 35.182241 40.44028 32 1770624 5577167 35.179838 40.437942 33 895455 139586 35.178428 40.438138 34 2578502 2955524 35.162346 40.428405 35 2312569 3928612 35.18153 40.440549 36 113810282 2318671 35.211455 40.461436 37 0 4339994 35.208356 40.461707 38 0 440623 35.209687 40.463394 39 0 5222508 35.200904 40.455131 40 0 2 35.19024 40.448972 41 0 370017576 35.175814 40.437883 42 0 0 35.173515 40.435246 43 0 0 35.173994 40.436491 44 0 0 35.184919 40.444065 45 0 0 35.195874 40.450612 46 0 0 35.193269 40.449259 47 0 0 35.182762 40.442883 48 0 0 35.173354 40.434751 49 0 0 35.167673 40.43018 50 0 0 35.167846 40.432966 51 0 0 35.159237 40.426239 52 0 0 35.15267 40.421408 53 0 0 35.14387 40.417413 54 0 0 35.13032 40.407952 55 0 0 35.133578 40.408756 56 0 0 35.103143 40.390435 57 0 0 35.102868 40.385437 58 0 0 35.079972 40.370692 59 0 0 35.057422 40.353435 60 0 0 35.027437 40.331329 61 0 0 34.984949 40.299183 62 0 0 34.946921 40.268843 63 0 0 34.889568 40.228158 64 0 0 34.853499 40.197672 65 0 0 34.791453 40.153113 66 0 0 34.721955 40.100924 67 0 0 34.649794 40.049025 68 0 0 34.575203 39.99348 69 0 0 34.489555 39.926972 70 0 0 34.407618 39.86088 71 0 0 34.309117 39.78391 72 0 0 34.221886 39.71131 73 0 0 34.121735 39.631868 74 0 0 34.028579 39.555378 75 0 0 33.9506 39.494416 76 0 0 33.857822 39.423451 77 0 0 33.783761 39.366548 78 0 0 33.702987 39.305799 79 0 0 33.63471 39.250283 80 0 0 33.575173 39.202189 81 0 0 33.515832 39.152591 82 0 0 33.458449 39.106046 83 0 0 33.406098 39.06276 84 0 0 33.379285 39.0381 85 0 0 33.332406 39.000286 86 0 0 33.285085 38.961455 87 0 0 33.248997 38.930681 88 0 0 33.196314 38.885928 89 0 0 33.148645 38.844757 90 0 0 33.101947 38.803783 91 0 0 33.06015 38.765367 92 0 0 33.00202 38.719222 93 0 0 32.972381 38.693713 94 0 0 32.939496 38.664925 95 0 0 32.90969 38.638461 96 0 0 32.902967 38.633462 97 0 0 32.880624 38.615386 98 0 0 32.888515 38.619985 99 0 0 32.902072 38.632077 100 0 0 32.941432 38.663426 101 0 0 32.979184 38.690693 102 0 0 33.01616 38.718227 103 0 0 33.06143 38.752644 104 0 0 33.060975 38.751361 105 0 0 33.083908 38.764482 106 0 0 33.102196 38.774322 107 0 0 33.087518 38.762696 108 0 0 33.062239 38.740557 109 0 0 33.053402 38.736916 110 0 0 33.019567 38.706249 111 0 0 32.9791 38.673802 112 0 0 32.933655 38.639638 113 0 0 32.883854 38.596687 114 0 0 32.810662 38.535591 115 0 0 32.770986 38.50258 116 0 0 32.733833 38.476212 117 0 0 32.724369 38.46984 118 0 0 32.723741 38.472274 119 0 0 32.736426 38.484506 120 0 0 32.749626 38.496111 121 0 0 32.763809 38.504185 122 0 0 32.786 38.526047 123 0 0 32.784384 38.517463 124 0 0 32.795617 38.523733 125 0 0 32.823375 38.542848 126 0 0 32.832862 38.545817 127 0 0 32.84892 38.554763 128 0 0 32.833196 38.54019 129 0 0 32.818705 38.524668 130 0 0 32.793918 38.507801 131 0 0 32.788077 38.50008 132 0 0 32.795022 38.501839 133 0 0 32.786303 38.497078 134 0 0 32.776416 38.486343 135 0 0 32.781728 38.485752 136 0 0 32.781976 38.484004 137 0 0 32.777831 38.485857 138 0 0 32.778923 38.484815 139 0 0 32.794555 38.505121 140 0 0 32.832507 38.533969 141 0 0 32.874423 38.565862 142 0 0 32.860786 38.556911 143 0 0 32.875488 38.566191 144 0 0 32.865079 38.553825 145 0 0 32.847874 38.539284 146 0 0 32.822328 38.511959 147 0 0 32.805201 38.496165 148 0 0 32.777038 38.472171 149 0 0 32.741969 38.444736 150 0 0 32.717589 38.420934 151 0 0 32.713911 38.423314 152 0 0 32.686954 38.399484 153 0 0 32.688639 38.40208 154 0 0 32.707273 38.415724 155 0 0 32.706714 38.420118 156 0 0 32.723696 38.427647 157 0 0 32.756631 38.456864 158 0 0 32.76153 38.457987 159 0 0 32.823297 38.507488 160 0 0 32.870917 38.542896 161 0 0 32.886239 38.553875 162 0 0 32.94861 38.604719 163 0 0 32.955493 38.609906 164 0 0 32.996549 38.639541 165 0 0 32.993303 38.63779 166 0 0 32.982831 38.629636 167 0 0 32.965744 38.611415 168 0 0 32.951728 38.596022 169 0 0 32.920318 38.567514 170 0 0 32.902216 38.554234 171 0 0 32.847761 38.510451 172 0 0 32.855671 38.514681 173 0 0 32.876925 38.538535 174 0 0 32.890018 38.548369 175 0 0 32.911673 38.571488 176 0 0 32.922693 38.579505 177 0 0 32.952324 38.603074 178 0 0 33.026269 38.664935 179 0 0 33.045007 38.683162 180 0 0 33.07628 38.706366 181 0 0 33.119262 38.74935 182 0 0 33.142996 38.766194 183 0 0 33.179273 38.799708 184 0 0 33.22908 38.840586 185 0 0 33.24297 38.854395 186 0 0 33.272552 38.881835 187 0 0 33.288059 38.89918 188 0 0 33.291809 38.899368 189 0 0 33.300857 38.905884 190 0 0 33.303336 38.910353 191 0 0 33.301227 38.911931 192 0 0 33.272311 38.890039 193 0 0 33.25769 38.883285 194 0 0 33.192787 38.836864 195 0 0 33.225123 38.868291 196 0 0 33.216387 38.87015 197 0 0 33.200603 38.861293 198 0 0 33.189707 38.859397 199 0 0 33.186033 38.857366 200 0 0 33.227964 38.89395 201 0 0 33.187248 38.879966 202 0 0 33.212627 38.892238 203 0 0 33.184231 38.880444 204 0 0 33.145329 38.866692 205 0 0 33.151559 38.871705 206 0 0 33.132037 38.860216 207 0 0 33.108815 38.8479 208 0 0 33.116981 38.85973 209 0 0 33.095926 38.842253 210 0 0 33.054298 38.82402 211 0 0 33.047032 38.820315 212 0 0 33.086923 38.856388 213 0 0 33.024523 38.81086 214 0 0 32.965792 38.758582 215 0 0 33.034521 38.815135 216 0 0 32.957337 38.768986 217 0 0 32.958476 38.766356 218 0 0 32.881295 38.718638 219 0 0 32.916166 38.740061 220 0 0 32.937206 38.764182 221 0 0 32.887378 38.736611 222 0 0 32.803766 38.667078 223 0 0 32.820237 38.676364 224 0 0 32.780656 38.652983 225 0 0 32.743643 38.621596 226 0 0 32.775482 38.658692 227 0 0 32.755858 38.639264 228 0 0 32.740261 38.631048 229 0 0 32.693366 38.596404 230 0 0 32.697485 38.607037 231 0 0 32.665148 38.595775 232 0 0 32.636588 38.565928 233 0 0 32.634628 38.564105 234 0 0 32.565072 38.525648 235 0 0 32.608336 38.552423 236 0 0 32.540144 38.509439 237 0 0 32.489894 38.472009 238 0 0 32.520482 38.498938 239 0 0 32.475456 38.481016 240 0 0 32.464524 38.480261 241 0 0 32.41134 38.438888 242 0 0 32.420908 38.446723 243 0 0 32.422934 38.43892 244 0 0 32.313478 38.372175 245 0 0 32.211508 38.296186 246 0 0 32.291197 38.355123 247 0 0 32.205882 38.289338 248 0 0 32.237392 38.321307 249 0 0 32.243035 38.324661 250 0 0 32.179306 38.286936 251 0 0 32.151678 38.273872 252 0 0 32.105166 38.234729 253 0 0 32.092502 38.232795 254 0 0 31.988988 38.179975 255 0 0 31.988072 38.17519 256 0 0 31.923398 38.119391 257 0 0 31.881541 38.079616 258 0 0 31.789948 38.033454 259 0 0 31.847054 38.062771 260 0 0 31.793804 38.04055 261 0 0 31.786494 38.033576 262 0 0 31.757113 38.027755 263 0 0 31.66431 37.953142 264 0 0 31.638162 37.922316 265 0 0 31.584165 37.907399 266 0 0 31.504808 37.863533 267 0 0 31.510479 37.867012 268 0 0 31.351061 37.754426 269 0 0 31.324243 37.737041 270 0 0 31.252295 37.679728 271 0 0 31.314017 37.739772 272 0 0 31.262301 37.692382 273 0 0 31.153328 37.636533 274 0 0 31.031446 37.533771 275 0 0 31.083722 37.570984 276 0 0 30.996478 37.514906 277 0 0 30.868244 37.454598 278 0 0 30.745641 37.342993 279 0 0 30.792318 37.391054 280 0 0 30.68815 37.335892 281 0 0 30.549366 37.214212 282 0 0 30.495169 37.221918 283 0 0 30.464432 37.17295 284 0 0 30.402915 37.129684 285 0 0 30.376917 37.107794 286 0 0 30.180745 36.973299 287 0 0 30.181153 36.953721 288 0 0 30.051507 36.884922 289 0 0 30.127086 36.926932 290 0 0 29.946284 36.832325 291 0 0 29.809864 36.728047 292 0 0 30.004754 36.828976 293 0 0 29.839175 36.739056 294 0 0 29.626644 36.567944 295 0 0 29.706772 36.643147 296 0 0 29.678593 36.62645 297 0 0 29.441057 36.445105 298 0 0 29.293004 36.364107 299 0 0 29.299248 36.343222 300 0 0 29.221384 36.274013 301 0 0 29.371475 36.389532 302 0 0 28.997203 36.177284 303 0 0 29.196638 36.273988 304 0 0 29.04648 36.173065 305 0 0 29.15756 36.234223 306 0 0 29.006906 36.182812 307 0 0 28.742381 36.000271 308 0 0 28.670256 35.920238 309 0 0 28.71055 35.934098 310 0 0 28.600488 35.823984 311 0 0 28.931334 36.068666 312 0 0 29.060023 36.189128 313 0 0 28.697376 35.905328 314 0 0 28.886097 36.047977 315 0 0 28.936776 36.085236 316 0 0 28.408257 35.680046 317 0 0 28.531835 35.795811 318 0 0 28.404708 35.587898 319 0 0 28.314258 35.731788 320 0 0 28.432185 35.704162 321 0 0 28.267889 35.651488 322 0 0 28.497061 35.779665 323 0 0 28.393723 35.707085 324 0 0 28.604101 35.847529 325 0 0 28.507826 35.685507 326 0 0 28.360431 35.75906 327 0 0 28.545552 35.744909 328 0 0 28.540732 35.812672 329 0 0 27.996042 35.358839 330 0 0 27.878223 35.378701 331 0 0 27.915739 35.401166 332 0 0 27.912886 35.353297 333 0 0 27.90121 35.227151 334 0 0 28.741419 35.927536 335 0 0 27.866841 35.303742 336 0 0 27.743284 35.248756 337 0 0 27.788732 35.134977 338 0 0 27.373494 34.752343 339 0 0 27.208889 34.734815 340 0 0 28.664948 36.063574 341 0 0 27.611765 35.080392 342 0 0 27.077922 34.928571 343 0 0 28.37594 35.553885 344 0 0 27.8 35.4 345 0 0 26.913462 34.676282 346 0 0 26.696629 34.7603 347 0 0 27.28 34.964444 348 0 0 27.1875 35.083333 349 0 0 27.111111 34.888889 350 0 0 28.816327 36.156463 351 0 0 27.738095 35.087302 352 0 0 31.157895 37.736842 353 0 0 28.705882 35.352941 354 0 0 26.266667 34.444444 355 0 0 28.307692 35.051282 356 0 0 27.909091 35.833333 357 0 0 30.666667 38.148148 358 0 0 27.0625 35.520833 359 0 0 22.928571 31.02381 360 0 0 29.583333 37.194444 361 0 0 26.727273 34.727273 362 0 0 25.666667 34.851852 363 0 0 26.888889 35.148148 364 0 0 23.75 30.541667 365 0 0 31 37.428571 366 0 0 27.333333 35.555556 367 0 0 27.2 35.8 368 0 0 34.6 39.666667 369 0 0 31.4 38.933333 370 0 0 36 40.833333 371 0 0 27.666667 32.444444 372 0 0 31 37.333333 373 0 0 36 41 374 0 0 36 41 375 0 0 27 35.5 376 0 0 29.5 37.333333 377 0 0 8 15.333333 378 0 0 29 37 379 0 0 15 25.666667 380 0 0 31 38 381 0 0 9 27.333333 382 0 0 29 37 383 0 0 26 33 384 0 0 23 35 385 0 0 23 35 386 0 0 21 32.666667 387 0 0 33 38.666667 388 0 0 10 30.666667 389 0 0 36 41 390 0 0 23 35 391 0 0 23 32 392 0 0 30 35.666667 393 0 0 10 30.666667