## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5288-Z0033-CATCATCGATTCGAT/441525-L5288-Z0033-CATCATCGATTCGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5288-Z0033-CATCATCGATTCGAT/441525-L5288-Z0033-CATCATCGATTCGAT_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 02:54:43 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 1000428 1000428 176 176305057 176305057 171601988 171601988 161953614 161953614 0 0 0.973324 0.918599 0 0.973324 0.918599 0 528915171 528915171 522844468 522844468 507678304 507678304 481060885 481060885 0.988522 0.959848 0.909524 0.988522 0.959848 0.909524 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 966 0 35.992611 40.994497 1 13554 0 35.986287 40.990634 2 16625 6472 35.994774 40.995465 3 39350 1629 35.982007 40.985487 4 56743 55181 35.989098 40.99095 5 117989 15668 35.994063 40.995156 6 94200 141645 35.968458 40.974433 7 200699 166886 35.978096 40.984661 8 167659 143526 35.988543 40.990696 9 234640 109281 35.938791 40.94869 10 241388 479086 35.894192 40.930929 11 286292 65221 35.93251 40.950884 12 329432 675966 35.542479 40.620106 13 322471 186627 34.598748 40.137745 14 442291 922449 35.881448 40.926486 15 370050 365439 35.836042 40.883713 16 350594 366745 35.783595 40.811309 17 499284 1002618 35.917135 40.932219 18 535967 705455 35.71732 40.777413 19 382875 660809 35.812677 40.866037 20 567183 940022 35.937127 40.957871 21 667454 1379001 35.853785 40.895851 22 364987 532000 35.661658 40.772695 23 1180880 1436123 35.424466 40.614238 24 604149 1246195 35.47055 40.641033 25 540340 518912 35.449369 40.628895 26 1854862 2598802 35.406945 40.596714 27 378651 984640 35.429492 40.617275 28 965511 433347 35.439466 40.624724 29 2524357 5097122 35.422981 40.611943 30 858904 51090 35.430898 40.616834 31 2578369 1056447 35.427846 40.613043 32 1886745 5331471 35.422492 40.608053 33 961082 151662 35.426196 40.612743 34 2730713 3171148 35.41272 40.604216 35 2543516 3843650 35.436195 40.619689 36 150394285 2595234 35.455213 40.632849 37 0 4367492 35.44576 40.627538 38 0 564055 35.437096 40.621512 39 0 5485170 35.438107 40.621876 40 0 9 35.430047 40.616551 41 0 481060876 35.419 40.607188 42 0 0 35.409838 40.601118 43 0 0 35.418257 40.606234 44 0 0 35.425179 40.610211 45 0 0 35.426192 40.611909 46 0 0 35.422002 40.608726 47 0 0 35.41569 40.604886 48 0 0 35.409692 40.601313 49 0 0 35.411761 40.602047 50 0 0 35.410226 40.60049 51 0 0 35.400227 40.594744 52 0 0 35.391133 40.587972 53 0 0 35.388109 40.587426 54 0 0 35.385655 40.584529 55 0 0 35.378436 40.579333 56 0 0 35.363742 40.570809 57 0 0 35.372606 40.575018 58 0 0 35.366017 40.569304 59 0 0 35.353776 40.560889 60 0 0 35.340946 40.550111 61 0 0 35.320189 40.535403 62 0 0 35.300347 40.51949 63 0 0 35.289021 40.510073 64 0 0 35.269335 40.495584 65 0 0 35.241491 40.475115 66 0 0 35.218536 40.457612 67 0 0 35.190274 40.436513 68 0 0 35.164015 40.417242 69 0 0 35.137178 40.397453 70 0 0 35.099083 40.367391 71 0 0 35.06374 40.338751 72 0 0 35.020616 40.305668 73 0 0 34.987189 40.277273 74 0 0 34.948722 40.247872 75 0 0 34.910901 40.218224 76 0 0 34.868027 40.184602 77 0 0 34.832537 40.157475 78 0 0 34.792084 40.124831 79 0 0 34.745552 40.090479 80 0 0 34.711351 40.063308 81 0 0 34.678245 40.034805 82 0 0 34.645186 40.009187 83 0 0 34.616525 39.983709 84 0 0 34.588467 39.96291 85 0 0 34.561877 39.940505 86 0 0 34.541282 39.923765 87 0 0 34.527458 39.91284 88 0 0 34.501192 39.889571 89 0 0 34.474464 39.868389 90 0 0 34.464275 39.861879 91 0 0 34.437805 39.83522 92 0 0 34.423738 39.823718 93 0 0 34.412614 39.812749 94 0 0 34.391923 39.79512 95 0 0 34.377437 39.78333 96 0 0 34.366524 39.774303 97 0 0 34.351448 39.759717 98 0 0 34.342836 39.754127 99 0 0 34.34096 39.751373 100 0 0 34.34681 39.758236 101 0 0 34.356169 39.764328 102 0 0 34.3598 39.765059 103 0 0 34.365247 39.769049 104 0 0 34.371859 39.772528 105 0 0 34.377024 39.774889 106 0 0 34.38327 39.778489 107 0 0 34.380675 39.777295 108 0 0 34.383628 39.780516 109 0 0 34.383845 39.781767 110 0 0 34.375565 39.773445 111 0 0 34.355591 39.75836 112 0 0 34.338668 39.741335 113 0 0 34.305735 39.711523 114 0 0 34.283875 39.693966 115 0 0 34.257392 39.671418 116 0 0 34.239138 39.656132 117 0 0 34.220495 39.645214 118 0 0 34.197226 39.629455 119 0 0 34.191865 39.628458 120 0 0 34.18338 39.621998 121 0 0 34.183805 39.622579 122 0 0 34.185684 39.622546 123 0 0 34.179574 39.613702 124 0 0 34.183873 39.614478 125 0 0 34.186043 39.61516 126 0 0 34.195817 39.622066 127 0 0 34.206797 39.627544 128 0 0 34.207318 39.628895 129 0 0 34.20601 39.629278 130 0 0 34.198851 39.624359 131 0 0 34.193083 39.619197 132 0 0 34.186535 39.613104 133 0 0 34.17872 39.603294 134 0 0 34.181545 39.606591 135 0 0 34.157462 39.581792 136 0 0 34.154342 39.577828 137 0 0 34.149515 39.576305 138 0 0 34.136349 39.566754 139 0 0 34.143399 39.575384 140 0 0 34.154507 39.587627 141 0 0 34.171719 39.601803 142 0 0 34.174985 39.604151 143 0 0 34.177023 39.603933 144 0 0 34.161866 39.590934 145 0 0 34.143582 39.572426 146 0 0 34.127015 39.557269 147 0 0 34.100925 39.534652 148 0 0 34.078406 39.518517 149 0 0 34.049918 39.49542 150 0 0 34.017541 39.469858 151 0 0 34.003267 39.458179 152 0 0 33.96817 39.433109 153 0 0 33.957434 39.424635 154 0 0 33.935457 39.405245 155 0 0 33.920807 39.39229 156 0 0 33.905488 39.376348 157 0 0 33.903746 39.374292 158 0 0 33.903604 39.375535 159 0 0 33.899687 39.370576 160 0 0 33.908924 39.379955 161 0 0 33.909138 39.379899 162 0 0 33.906057 39.379037 163 0 0 33.928072 39.394524 164 0 0 33.915699 39.382499 165 0 0 33.893408 39.364349 166 0 0 33.855132 39.335102 167 0 0 33.821332 39.301163 168 0 0 33.760804 39.249179 169 0 0 33.693622 39.190166 170 0 0 33.641016 39.144153 171 0 0 33.594278 39.107862 172 0 0 33.542057 39.062766 173 0 0 33.509297 39.040601 174 0 0 33.477155 39.013592 175 0 0 33.459678 39.002829 176 0 0 33.441552 38.984353 177 0 0 33.444453 38.98454 178 0 0 33.441786 38.982155 179 0 0 33.452099 38.990876 180 0 0 33.459009 38.998437 181 0 0 33.476903 39.011534 182 0 0 33.502819 39.037689 183 0 0 33.527219 39.057052 184 0 0 33.552122 39.074928 185 0 0 33.579745 39.095164 186 0 0 33.589858 39.108263 187 0 0 33.614305 39.12461 188 0 0 33.622793 39.129357 189 0 0 33.623813 39.132481 190 0 0 33.623483 39.132672 191 0 0 33.609671 39.122706 192 0 0 33.600945 39.119357 193 0 0 33.568351 39.096519 194 0 0 33.54739 39.082692 195 0 0 33.532977 39.07877 196 0 0 33.527942 39.082425 197 0 0 33.498545 39.059108 198 0 0 33.498921 39.063569 199 0 0 33.489168 39.063969 200 0 0 33.448278 39.035909 201 0 0 33.450359 39.045366 202 0 0 33.412278 39.018834 203 0 0 33.374962 39.001586 204 0 0 33.365216 39.001029 205 0 0 33.344767 38.991056 206 0 0 33.311185 38.971463 207 0 0 33.293029 38.963015 208 0 0 33.266816 38.94984 209 0 0 33.254172 38.947863 210 0 0 33.200707 38.907949 211 0 0 33.161857 38.890547 212 0 0 33.176794 38.900096 213 0 0 33.117991 38.863789 214 0 0 33.100392 38.859104 215 0 0 33.077909 38.8435 216 0 0 33.021229 38.80491 217 0 0 33.007953 38.79819 218 0 0 33.001925 38.7973 219 0 0 32.970388 38.778202 220 0 0 32.960821 38.771278 221 0 0 32.944461 38.766304 222 0 0 32.891926 38.728919 223 0 0 32.874274 38.719009 224 0 0 32.843818 38.695068 225 0 0 32.817103 38.678068 226 0 0 32.804844 38.673291 227 0 0 32.777046 38.658338 228 0 0 32.771817 38.656889 229 0 0 32.713211 38.613828 230 0 0 32.698971 38.613285 231 0 0 32.668044 38.585276 232 0 0 32.645955 38.576441 233 0 0 32.632473 38.569636 234 0 0 32.597802 38.540265 235 0 0 32.579134 38.533528 236 0 0 32.53496 38.501691 237 0 0 32.525841 38.49839 238 0 0 32.484207 38.484482 239 0 0 32.448572 38.455655 240 0 0 32.443419 38.449745 241 0 0 32.378287 38.404372 242 0 0 32.355897 38.396965 243 0 0 32.311553 38.361223 244 0 0 32.317887 38.378825 245 0 0 32.274169 38.343851 246 0 0 32.253575 38.333527 247 0 0 32.243046 38.329626 248 0 0 32.19979 38.306848 249 0 0 32.15882 38.28075 250 0 0 32.154489 38.281377 251 0 0 32.106149 38.238271 252 0 0 32.084053 38.228202 253 0 0 32.063804 38.217111 254 0 0 31.98888 38.172833 255 0 0 31.930669 38.14127 256 0 0 31.872288 38.097011 257 0 0 31.886763 38.110615 258 0 0 31.830344 38.074377 259 0 0 31.773563 38.028494 260 0 0 31.737726 38.020224 261 0 0 31.689349 37.985185 262 0 0 31.72272 38.006275 263 0 0 31.635727 37.952427 264 0 0 31.568339 37.890972 265 0 0 31.519188 37.878762 266 0 0 31.504128 37.864965 267 0 0 31.394331 37.793041 268 0 0 31.395815 37.794242 269 0 0 31.35286 37.776142 270 0 0 31.236535 37.682997 271 0 0 31.239561 37.703129 272 0 0 31.18247 37.648381 273 0 0 31.095206 37.590443 274 0 0 31.010731 37.535134 275 0 0 30.936981 37.499251 276 0 0 30.872042 37.450914 277 0 0 30.743029 37.358512 278 0 0 30.728388 37.324358 279 0 0 30.690139 37.31926 280 0 0 30.641419 37.287647 281 0 0 30.554191 37.233646 282 0 0 30.537269 37.226984 283 0 0 30.426762 37.131172 284 0 0 30.373661 37.103435 285 0 0 30.3003 37.060466 286 0 0 30.333149 37.08662 287 0 0 30.147081 36.966026 288 0 0 30.127127 36.940392 289 0 0 30.107421 36.934805 290 0 0 30.043284 36.879345 291 0 0 29.898935 36.782342 292 0 0 29.889686 36.77289 293 0 0 29.762285 36.683617 294 0 0 29.673923 36.619345 295 0 0 29.714526 36.663271 296 0 0 29.549451 36.534473 297 0 0 29.534269 36.527512 298 0 0 29.523495 36.521656 299 0 0 29.552112 36.538392 300 0 0 29.4574 36.457775 301 0 0 29.367107 36.385525 302 0 0 29.391049 36.426184 303 0 0 29.273952 36.344183 304 0 0 29.271743 36.348526 305 0 0 29.166881 36.272396 306 0 0 29.12883 36.224225 307 0 0 29.11321 36.219667 308 0 0 29.070792 36.196545 309 0 0 29.003118 36.158299 310 0 0 29.088829 36.20896 311 0 0 28.964675 36.122272 312 0 0 28.95948 36.110066 313 0 0 28.759128 35.983446 314 0 0 28.797641 35.987127 315 0 0 28.78298 35.987302 316 0 0 28.820287 36.030812 317 0 0 28.83173 36.037321 318 0 0 28.77248 36.006862 319 0 0 28.669581 35.879575 320 0 0 28.752315 35.946955 321 0 0 28.765751 35.95987 322 0 0 28.647873 35.869447 323 0 0 28.533175 35.811824 324 0 0 28.403516 35.743641 325 0 0 28.514204 35.810321 326 0 0 28.614286 35.886037 327 0 0 28.344642 35.677796 328 0 0 28.414235 35.672226 329 0 0 28.272217 35.655765 330 0 0 28.406088 35.723954 331 0 0 28.475934 35.851452 332 0 0 28.482759 35.848582 333 0 0 28.155844 35.565887 334 0 0 28.65848 35.925146 335 0 0 28.088742 35.392494 336 0 0 27.995565 35.459226 337 0 0 28.217244 35.662722 338 0 0 27.622498 35.125199 339 0 0 28.046237 35.413978 340 0 0 28.153846 35.486378 341 0 0 27.754667 35.148444 342 0 0 28.6049 35.869832 343 0 0 27.759099 35.159445 344 0 0 28.107071 35.575758 345 0 0 28.122727 35.508333 346 0 0 27.745547 35.2324 347 0 0 27.452096 34.94012 348 0 0 28.877622 36.04662 349 0 0 28.226721 35.663968 350 0 0 28.050459 35.411315 351 0 0 27.064865 34.436036 352 0 0 27.630573 35.006369 353 0 0 28.142857 35.561905 354 0 0 27.909836 35.726776 355 0 0 26.87156 34.892966 356 0 0 27.737374 35.329966 357 0 0 29 36.286275 358 0 0 27.291667 34.935185 359 0 0 27.514706 35.02451 360 0 0 27.310345 35.109195 361 0 0 28.849057 36.220126 362 0 0 25.612245 33.564626 363 0 0 29.341463 36.674797 364 0 0 26.435897 34.512821 365 0 0 25.942857 34.180952 366 0 0 29.125 35.875 367 0 0 26.758621 34.735632 368 0 0 29.777778 36.91358 369 0 0 27.363636 35.787879 370 0 0 29 37.037037 371 0 0 26.4 34.177778 372 0 0 27.692308 35.948718 373 0 0 27.75 35.5 374 0 0 27.7 35.4 375 0 0 29.75 37.125 376 0 0 29.25 37.25 377 0 0 24.6 33.6 378 0 0 32 38.5 379 0 0 24.666667 34.888889 380 0 0 28 35.333333 381 0 0 35.666667 40.555556 382 0 0 35 39.444444 383 0 0 27.333333 32.888889 384 0 0 31 37.666667 385 0 0 22 29.555556 386 0 0 31 37.444444 387 0 0 29.5 36 388 0 0 28 35 389 0 0 26.5 33.333333 390 0 0 24.5 33.666667 391 0 0 36 41 392 0 0 23 35 393 0 0 4 8.666667 394 0 0 12 31.333333 395 0 0 29 35 396 0 0 29 35