## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5284-Z0028-CAGACTTGCTGCGAT/441525-L5284-Z0028-CAGACTTGCTGCGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5284-Z0028-CAGACTTGCTGCGAT/441525-L5284-Z0028-CAGACTTGCTGCGAT_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 02:56:50 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 1000517 1000517 170 170567218 170567218 165863469 165863469 156286840 156286840 0 0 0.972423 0.916277 0 0.972423 0.916277 0 511701654 511701654 505615343 505615343 490527516 490527516 464357051 464357051 0.988106 0.95862 0.907476 0.988106 0.95862 0.907476 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 1016 1 35.993328 40.994878 1 12877 1 35.984766 40.989599 2 15622 6061 35.993082 40.994176 3 37881 1581 35.981996 40.985284 4 56974 52863 35.988783 40.990873 5 117270 15859 35.993649 40.994828 6 98904 137372 35.97413 40.979121 7 199617 165045 35.977146 40.984494 8 172156 145877 35.984542 40.987307 9 233504 107323 35.936567 40.946538 10 240610 489372 35.912009 40.940115 11 282425 63578 35.945213 40.961036 12 326989 678875 35.50697 40.588622 13 323436 187928 34.480167 40.065734 14 439258 923431 35.886816 40.929888 15 366275 363616 35.824314 40.876821 16 352681 373689 35.787896 40.815033 17 503925 1010880 35.920097 40.935371 18 538174 704811 35.693642 40.753591 19 384155 658148 35.802229 40.856454 20 555509 951426 35.936448 40.957153 21 666594 1374561 35.847123 40.890641 22 360351 531786 35.655203 40.769095 23 1165544 1398403 35.425586 40.618858 24 602729 1232863 35.472095 40.643222 25 541909 514805 35.451733 40.631657 26 1850744 2604660 35.413397 40.603811 27 373192 970942 35.438114 40.622178 28 951529 425726 35.447521 40.629491 29 2508528 5082655 35.43692 40.621452 30 836925 49582 35.425408 40.61248 31 2519757 1024735 35.432026 40.615044 32 1839857 5304333 35.437573 40.619318 33 932515 147293 35.422538 40.610401 34 2681208 3066234 35.419864 40.608492 35 2493850 3809994 35.436609 40.618859 36 144982728 2523283 35.45505 40.63109 37 0 4324418 35.449016 40.629366 38 0 527140 35.440635 40.624672 39 0 5393453 35.435558 40.620463 40 0 2 35.431374 40.615811 41 0 464357049 35.420416 40.609437 42 0 0 35.412527 40.602655 43 0 0 35.416743 40.604866 44 0 0 35.433037 40.615409 45 0 0 35.428822 40.614063 46 0 0 35.427235 40.610949 47 0 0 35.420168 40.607919 48 0 0 35.412605 40.601516 49 0 0 35.409987 40.600778 50 0 0 35.410997 40.600571 51 0 0 35.403936 40.595774 52 0 0 35.396678 40.59176 53 0 0 35.394368 40.589347 54 0 0 35.386843 40.585203 55 0 0 35.386864 40.584695 56 0 0 35.378095 40.578765 57 0 0 35.376701 40.577282 58 0 0 35.366286 40.56949 59 0 0 35.352196 40.55997 60 0 0 35.342848 40.552259 61 0 0 35.334232 40.545695 62 0 0 35.311811 40.528166 63 0 0 35.294804 40.516265 64 0 0 35.273758 40.500413 65 0 0 35.255613 40.487372 66 0 0 35.232534 40.470576 67 0 0 35.204231 40.449472 68 0 0 35.171406 40.425215 69 0 0 35.135458 40.397384 70 0 0 35.101273 40.371549 71 0 0 35.058827 40.337124 72 0 0 35.008095 40.297473 73 0 0 34.967845 40.264505 74 0 0 34.923122 40.228818 75 0 0 34.878735 40.193437 76 0 0 34.831302 40.15755 77 0 0 34.780344 40.118944 78 0 0 34.739528 40.087864 79 0 0 34.688093 40.045874 80 0 0 34.643189 40.011662 81 0 0 34.598295 39.973946 82 0 0 34.562623 39.945681 83 0 0 34.529803 39.919505 84 0 0 34.49868 39.895427 85 0 0 34.473965 39.876377 86 0 0 34.44662 39.855131 87 0 0 34.425447 39.835612 88 0 0 34.401022 39.815027 89 0 0 34.367924 39.788397 90 0 0 34.355162 39.775563 91 0 0 34.321885 39.747617 92 0 0 34.293803 39.724095 93 0 0 34.280351 39.710693 94 0 0 34.257958 39.690692 95 0 0 34.240894 39.677901 96 0 0 34.227887 39.666289 97 0 0 34.201336 39.645116 98 0 0 34.19951 39.644547 99 0 0 34.199884 39.642846 100 0 0 34.210551 39.652408 101 0 0 34.216865 39.65658 102 0 0 34.231922 39.666093 103 0 0 34.245376 39.675331 104 0 0 34.249579 39.677003 105 0 0 34.264497 39.687621 106 0 0 34.261774 39.686536 107 0 0 34.264403 39.685909 108 0 0 34.270359 39.69201 109 0 0 34.261541 39.68581 110 0 0 34.246438 39.672923 111 0 0 34.219448 39.654164 112 0 0 34.192175 39.627397 113 0 0 34.155858 39.596748 114 0 0 34.11792 39.565883 115 0 0 34.095067 39.545426 116 0 0 34.060271 39.518464 117 0 0 34.041096 39.505612 118 0 0 34.026258 39.497943 119 0 0 34.022992 39.495314 120 0 0 34.018091 39.492194 121 0 0 34.02266 39.494698 122 0 0 34.015452 39.489365 123 0 0 34.010895 39.482135 124 0 0 34.012607 39.482741 125 0 0 34.016548 39.48421 126 0 0 34.016895 39.481638 127 0 0 34.028413 39.487933 128 0 0 34.008453 39.468905 129 0 0 34.00816 39.469706 130 0 0 33.987891 39.453914 131 0 0 33.980515 39.448539 132 0 0 33.961526 39.431354 133 0 0 33.96177 39.431598 134 0 0 33.942921 39.415401 135 0 0 33.938908 39.410056 136 0 0 33.921238 39.395704 137 0 0 33.911692 39.387371 138 0 0 33.892609 39.374428 139 0 0 33.907096 39.388239 140 0 0 33.915203 39.395434 141 0 0 33.911093 39.391519 142 0 0 33.920497 39.399137 143 0 0 33.914112 39.392442 144 0 0 33.898395 39.380721 145 0 0 33.897219 39.372164 146 0 0 33.862701 39.346405 147 0 0 33.823912 39.314348 148 0 0 33.817428 39.307705 149 0 0 33.78789 39.282254 150 0 0 33.736497 39.242776 151 0 0 33.723919 39.231225 152 0 0 33.697103 39.214106 153 0 0 33.672644 39.193106 154 0 0 33.648067 39.172893 155 0 0 33.657508 39.18097 156 0 0 33.637216 39.161744 157 0 0 33.64728 39.169341 158 0 0 33.63722 39.160536 159 0 0 33.64115 39.161938 160 0 0 33.653464 39.17102 161 0 0 33.673491 39.187289 162 0 0 33.660074 39.177538 163 0 0 33.659607 39.175862 164 0 0 33.668503 39.184593 165 0 0 33.655372 39.174652 166 0 0 33.618106 39.141745 167 0 0 33.594489 39.11928 168 0 0 33.557358 39.08546 169 0 0 33.488059 39.02684 170 0 0 33.453331 38.995012 171 0 0 33.411968 38.96436 172 0 0 33.388444 38.944601 173 0 0 33.372057 38.931712 174 0 0 33.353999 38.915423 175 0 0 33.355896 38.918704 176 0 0 33.343675 38.907061 177 0 0 33.365319 38.924288 178 0 0 33.373626 38.934743 179 0 0 33.377865 38.936485 180 0 0 33.407328 38.960218 181 0 0 33.444844 38.995086 182 0 0 33.481997 39.023038 183 0 0 33.508039 39.048929 184 0 0 33.533193 39.065628 185 0 0 33.553128 39.085671 186 0 0 33.575771 39.106026 187 0 0 33.592065 39.1175 188 0 0 33.592685 39.114321 189 0 0 33.602734 39.127812 190 0 0 33.601893 39.125818 191 0 0 33.587749 39.116514 192 0 0 33.571969 39.109581 193 0 0 33.544058 39.09047 194 0 0 33.540445 39.093052 195 0 0 33.527596 39.090618 196 0 0 33.513963 39.081575 197 0 0 33.505862 39.080624 198 0 0 33.493662 39.074789 199 0 0 33.457003 39.051244 200 0 0 33.456242 39.05861 201 0 0 33.427202 39.04437 202 0 0 33.411698 39.043726 203 0 0 33.416557 39.04794 204 0 0 33.38815 39.034613 205 0 0 33.382255 39.036324 206 0 0 33.374075 39.036356 207 0 0 33.333933 39.006771 208 0 0 33.30037 38.992848 209 0 0 33.294363 38.989942 210 0 0 33.233821 38.949976 211 0 0 33.211943 38.935005 212 0 0 33.209244 38.938312 213 0 0 33.191433 38.92707 214 0 0 33.146843 38.903276 215 0 0 33.11811 38.880858 216 0 0 33.081224 38.858745 217 0 0 33.078109 38.863481 218 0 0 33.053374 38.844939 219 0 0 33.047962 38.843088 220 0 0 33.007349 38.814912 221 0 0 32.998103 38.815924 222 0 0 32.946772 38.77608 223 0 0 32.957349 38.792031 224 0 0 32.922892 38.761286 225 0 0 32.893135 38.7429 226 0 0 32.881666 38.740193 227 0 0 32.836562 38.711779 228 0 0 32.801606 38.685202 229 0 0 32.823745 38.706816 230 0 0 32.795071 38.683084 231 0 0 32.743606 38.651849 232 0 0 32.744244 38.65543 233 0 0 32.668208 38.605154 234 0 0 32.664142 38.606134 235 0 0 32.636869 38.584772 236 0 0 32.611578 38.56938 237 0 0 32.601899 38.565288 238 0 0 32.542651 38.533804 239 0 0 32.474895 38.482529 240 0 0 32.472926 38.477623 241 0 0 32.466824 38.471603 242 0 0 32.435914 38.46481 243 0 0 32.404801 38.446668 244 0 0 32.395074 38.431509 245 0 0 32.34534 38.406176 246 0 0 32.287762 38.357465 247 0 0 32.29775 38.381566 248 0 0 32.249713 38.347836 249 0 0 32.215207 38.31883 250 0 0 32.202833 38.307627 251 0 0 32.180817 38.299856 252 0 0 32.134035 38.26647 253 0 0 32.087608 38.241156 254 0 0 32.059217 38.229878 255 0 0 32.029706 38.212808 256 0 0 31.980405 38.171992 257 0 0 31.948964 38.149031 258 0 0 31.904756 38.122554 259 0 0 31.88374 38.118475 260 0 0 31.89761 38.125735 261 0 0 31.781482 38.042019 262 0 0 31.764333 38.045682 263 0 0 31.750353 38.043496 264 0 0 31.628906 37.964577 265 0 0 31.653102 37.964439 266 0 0 31.611593 37.944069 267 0 0 31.530112 37.890322 268 0 0 31.456188 37.835393 269 0 0 31.395387 37.803512 270 0 0 31.360899 37.775965 271 0 0 31.29429 37.731168 272 0 0 31.274361 37.713089 273 0 0 31.206128 37.679946 274 0 0 31.085748 37.595681 275 0 0 31.034118 37.563251 276 0 0 30.994904 37.534779 277 0 0 30.912894 37.477642 278 0 0 30.861035 37.442377 279 0 0 30.702368 37.322928 280 0 0 30.709483 37.327055 281 0 0 30.672853 37.314565 282 0 0 30.623781 37.301182 283 0 0 30.565785 37.241098 284 0 0 30.38522 37.109074 285 0 0 30.34244 37.077333 286 0 0 30.269019 37.044453 287 0 0 30.258053 37.021661 288 0 0 30.17398 36.969205 289 0 0 30.19251 36.977869 290 0 0 30.037895 36.873116 291 0 0 29.966449 36.821263 292 0 0 29.962748 36.832893 293 0 0 29.925309 36.790677 294 0 0 29.767669 36.691679 295 0 0 29.754682 36.676828 296 0 0 29.720896 36.643679 297 0 0 29.656711 36.602091 298 0 0 29.557142 36.508498 299 0 0 29.437787 36.453101 300 0 0 29.494244 36.470808 301 0 0 29.354986 36.411394 302 0 0 29.291747 36.348686 303 0 0 29.276391 36.361853 304 0 0 29.112467 36.222833 305 0 0 29.280898 36.33358 306 0 0 29.09763 36.185525 307 0 0 29.026881 36.144442 308 0 0 29.016483 36.167369 309 0 0 28.953218 36.111891 310 0 0 28.904523 36.058703 311 0 0 28.782528 35.981321 312 0 0 28.841972 36.023546 313 0 0 28.811699 35.985165 314 0 0 28.896707 36.046248 315 0 0 28.794095 35.948218 316 0 0 28.715859 35.91218 317 0 0 28.708151 35.908174 318 0 0 28.754751 35.948668 319 0 0 28.495072 35.781574 320 0 0 28.457298 35.758926 321 0 0 28.575917 35.891606 322 0 0 28.47019 35.776084 323 0 0 28.274021 35.584627 324 0 0 28.307144 35.613949 325 0 0 28.217596 35.589807 326 0 0 28.200397 35.614583 327 0 0 28.562279 35.803125 328 0 0 28.390479 35.686954 329 0 0 28.28263 35.736743 330 0 0 28.252865 35.615034 331 0 0 28.088492 35.544107 332 0 0 28.110851 35.440287 333 0 0 28.353439 35.628748 334 0 0 27.684706 35.14451 335 0 0 27.812085 35.355467 336 0 0 27.93646 35.368129 337 0 0 27.849832 35.25 338 0 0 27.637476 35.219397 339 0 0 27.923243 35.206847 340 0 0 27.908176 35.336268 341 0 0 28.077904 35.503305 342 0 0 28.204959 35.608815 343 0 0 27.981308 35.386916 344 0 0 28.303226 35.656631 345 0 0 27.770936 35.106732 346 0 0 27.40884 35.002762 347 0 0 28.061728 35.386831 348 0 0 28.958042 36.149184 349 0 0 28.680162 35.97166 350 0 0 29.070093 36.691589 351 0 0 28.933333 36.147009 352 0 0 28.169591 35.690058 353 0 0 28.517007 35.698413 354 0 0 27.212598 34.889764 355 0 0 27.741379 35.353448 356 0 0 27.53271 35 357 0 0 27.252525 34.93266 358 0 0 28.842697 36.116105 359 0 0 27.87013 35.510823 360 0 0 27.611111 34.893519 361 0 0 27.833333 35.313131 362 0 0 26.75 34.385417 363 0 0 26.766667 34.583333 364 0 0 27.017857 35.059524 365 0 0 29.510204 36.62585 366 0 0 26.571429 34.547619 367 0 0 26.2 34.391667 368 0 0 28.361111 35.657407 369 0 0 28 35.612903 370 0 0 27.548387 35.27957 371 0 0 28.25 35.97619 372 0 0 25.041667 33.75 373 0 0 26.791667 34.736111 374 0 0 27.318182 35.454545 375 0 0 23.7 33.116667 376 0 0 28.444444 35.777778 377 0 0 23.857143 33.47619 378 0 0 28.166667 35.805556 379 0 0 28.181818 36.454545 380 0 0 34.1 39.933333 381 0 0 32.2 38.133333 382 0 0 28 36.111111 383 0 0 29.25 35.666667 384 0 0 30.428571 37.238095 385 0 0 26.666667 34.722222 386 0 0 20 30.333333 387 0 0 29.833333 36.055556 388 0 0 28 34.25 389 0 0 32.75 38.5 390 0 0 34 39.833333 391 0 0 21.5 32 392 0 0 22 31.666667 393 0 0 36 41 394 0 0 36 40.666667 395 0 0 18 24.5 396 0 0 36 41 397 0 0 28.5 35.666667 398 0 0 36 41 399 0 0 36 41 400 0 0 31 37 401 0 0 36 41 402 0 0 34.5 40 403 0 0 15.5 26.333333 404 0 0 36 41