## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5417-Z0114-CAACATACATCAGAT/441525-L5417-Z0114-CAACATACATCAGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5417-Z0114-CAACATACATCAGAT/441525-L5417-Z0114-CAACATACATCAGAT_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 03:01:56 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 1000148 1000148 112 112531160 112531160 107588442 107588442 98565811 98565811 0 0 0.956077 0.875898 0 0.956077 0.875898 0 337593480 337593480 330917398 330917398 316569468 316569468 293345704 293345704 0.980224 0.937724 0.868932 0.980224 0.937724 0.868932 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 937 0 35.991288 40.993812 1 10248 0 35.98131 40.987829 2 13088 4040 35.993401 40.994899 3 33149 1077 35.982015 40.985631 4 54362 44282 35.991019 40.992959 5 107194 18942 35.994349 40.995548 6 115606 119217 35.97876 40.982316 7 190423 159112 35.976528 40.984491 8 212144 146956 35.985742 40.988314 9 244474 112159 35.960916 40.96718 10 263634 512306 35.886073 40.931842 11 309846 60844 35.913706 40.936931 12 363490 733852 35.138999 40.275131 13 360194 229142 33.407627 39.402905 14 472466 1039752 35.865154 40.916881 15 376376 389072 35.836017 40.881999 16 395428 488135 35.801808 40.823343 17 512486 1152433 35.889523 40.905713 18 553961 749947 35.776425 40.814385 19 353212 714814 35.737679 40.805823 20 495284 1008300 35.882005 40.92352 21 659484 1340132 35.816759 40.870919 22 303894 551427 35.506002 40.671488 23 1019030 1177539 35.137512 40.425408 24 556473 1120060 35.123495 40.413654 25 533986 439634 35.141054 40.426531 26 1741527 2517809 35.06736 40.370076 27 344384 798782 35.092391 40.385695 28 938639 358759 35.135628 40.414113 29 2429930 5035488 35.142629 40.419667 30 704410 38152 35.135254 40.41199 31 2215333 715276 35.127033 40.404508 32 1490871 5378433 35.120561 40.399598 33 790706 120455 35.116447 40.395433 34 2293268 2405681 35.114797 40.395511 35 2001716 3705103 35.128422 40.404154 36 89069507 1955519 35.15946 40.42607 37 0 3999467 35.161996 40.428255 38 0 311784 35.149657 40.419515 39 0 4593894 35.150711 40.420445 40 0 0 35.152942 40.420887 41 0 293345704 35.13977 40.412397 42 0 0 35.132927 40.406306 43 0 0 35.139019 40.411602 44 0 0 35.147729 40.416805 45 0 0 35.14728 40.417019 46 0 0 35.137749 40.409355 47 0 0 35.124934 40.400413 48 0 0 35.115919 40.394262 49 0 0 35.103503 40.384721 50 0 0 35.0853 40.374169 51 0 0 35.070002 40.362152 52 0 0 35.045616 40.345321 53 0 0 35.022713 40.328733 54 0 0 34.996648 40.30864 55 0 0 34.95141 40.275905 56 0 0 34.885989 40.228272 57 0 0 34.833727 40.190117 58 0 0 34.738814 40.122453 59 0 0 34.640959 40.050609 60 0 0 34.533061 39.970901 61 0 0 34.397076 39.868528 62 0 0 34.243357 39.747374 63 0 0 34.099569 39.63733 64 0 0 33.926577 39.501631 65 0 0 33.733718 39.360045 66 0 0 33.559874 39.22644 67 0 0 33.357992 39.074216 68 0 0 33.175511 38.934894 69 0 0 32.977418 38.778028 70 0 0 32.776289 38.621711 71 0 0 32.603592 38.478494 72 0 0 32.438457 38.345543 73 0 0 32.286986 38.221898 74 0 0 32.158741 38.122828 75 0 0 32.067068 38.046695 76 0 0 32.00277 37.995579 77 0 0 31.947141 37.951208 78 0 0 31.910494 37.921992 79 0 0 31.867917 37.885323 80 0 0 31.864663 37.874408 81 0 0 31.857213 37.862248 82 0 0 31.881385 37.872996 83 0 0 31.856809 37.848164 84 0 0 31.875594 37.859651 85 0 0 31.863461 37.845536 86 0 0 31.830153 37.812685 87 0 0 31.804237 37.790956 88 0 0 31.769752 37.755695 89 0 0 31.73212 37.723122 90 0 0 31.687215 37.682771 91 0 0 31.670447 37.665703 92 0 0 31.647555 37.63995 93 0 0 31.628494 37.624654 94 0 0 31.612725 37.611621 95 0 0 31.600962 37.602245 96 0 0 31.616343 37.616374 97 0 0 31.640757 37.63375 98 0 0 31.663957 37.649059 99 0 0 31.724542 37.700394 100 0 0 31.792593 37.753409 101 0 0 31.8746 37.816634 102 0 0 31.943634 37.871573 103 0 0 31.991168 37.906445 104 0 0 32.038602 37.941009 105 0 0 32.0531 37.942769 106 0 0 32.046483 37.938669 107 0 0 32.029811 37.922199 108 0 0 32.004848 37.900974 109 0 0 31.969818 37.868646 110 0 0 31.929399 37.839819 111 0 0 31.873629 37.795256 112 0 0 31.829191 37.764186 113 0 0 31.769173 37.712552 114 0 0 31.68523 37.650067 115 0 0 31.64431 37.617165 116 0 0 31.616162 37.593727 117 0 0 31.61782 37.596152 118 0 0 31.615751 37.593254 119 0 0 31.643833 37.616473 120 0 0 31.674125 37.638961 121 0 0 31.696586 37.65212 122 0 0 31.712107 37.668801 123 0 0 31.751897 37.696048 124 0 0 31.780274 37.71448 125 0 0 31.811836 37.737598 126 0 0 31.826042 37.742836 127 0 0 31.797911 37.721971 128 0 0 31.815019 37.727858 129 0 0 31.779085 37.690007 130 0 0 31.742343 37.660255 131 0 0 31.71996 37.643074 132 0 0 31.749927 37.663588 133 0 0 31.747037 37.662776 134 0 0 31.743925 37.657798 135 0 0 31.738542 37.655535 136 0 0 31.744627 37.660255 137 0 0 31.774421 37.678327 138 0 0 31.812425 37.714173 139 0 0 31.849355 37.742181 140 0 0 31.874849 37.769712 141 0 0 31.918961 37.80013 142 0 0 31.938824 37.812087 143 0 0 31.934286 37.807945 144 0 0 31.978896 37.843697 145 0 0 31.987289 37.845185 146 0 0 31.971179 37.840851 147 0 0 31.940581 37.810142 148 0 0 31.912461 37.788259 149 0 0 31.927605 37.796346 150 0 0 31.882042 37.758584 151 0 0 31.84488 37.724566 152 0 0 31.837277 37.72159 153 0 0 31.850128 37.728764 154 0 0 31.838416 37.72533 155 0 0 31.892319 37.764536 156 0 0 31.932331 37.810485 157 0 0 31.970979 37.838589 158 0 0 32.059095 37.908119 159 0 0 32.089397 37.93139 160 0 0 32.177772 37.997349 161 0 0 32.199205 38.01321 162 0 0 32.232392 38.036553 163 0 0 32.288887 38.089045 164 0 0 32.342348 38.125175 165 0 0 32.41066 38.189136 166 0 0 32.428974 38.198616 167 0 0 32.433086 38.197416 168 0 0 32.454175 38.210822 169 0 0 32.422373 38.187693 170 0 0 32.428793 38.189054 171 0 0 32.450111 38.203602 172 0 0 32.450639 38.214625 173 0 0 32.510808 38.26644 174 0 0 32.511298 38.259943 175 0 0 32.509823 38.264778 176 0 0 32.537328 38.295845 177 0 0 32.546393 38.30835 178 0 0 32.626778 38.376842 179 0 0 32.717796 38.446926 180 0 0 32.778649 38.507139 181 0 0 32.86199 38.563442 182 0 0 32.893776 38.599715 183 0 0 32.884952 38.596077 184 0 0 32.957097 38.649491 185 0 0 32.94632 38.626678 186 0 0 32.963373 38.650054 187 0 0 33.033516 38.703599 188 0 0 33.053288 38.727921 189 0 0 33.063538 38.740264 190 0 0 33.063317 38.752854 191 0 0 33.123746 38.799209 192 0 0 33.135257 38.818488 193 0 0 33.12072 38.797079 194 0 0 33.137353 38.825956 195 0 0 33.056233 38.757302 196 0 0 33.072644 38.778116 197 0 0 33.158998 38.848518 198 0 0 33.154308 38.874779 199 0 0 33.052144 38.782274 200 0 0 33.158426 38.856803 201 0 0 33.080909 38.833269 202 0 0 33.162321 38.886723 203 0 0 33.138505 38.879384 204 0 0 33.163469 38.893656 205 0 0 33.163465 38.89776 206 0 0 33.090425 38.85532 207 0 0 33.139329 38.889219 208 0 0 33.120827 38.874255 209 0 0 33.122529 38.870998 210 0 0 33.05217 38.843346 211 0 0 33.012624 38.824179 212 0 0 33.07046 38.861187 213 0 0 33.13473 38.893649 214 0 0 33.141264 38.90181 215 0 0 33.020259 38.837429 216 0 0 33.129647 38.878472 217 0 0 33.106191 38.904566 218 0 0 33.120977 38.910544 219 0 0 33.037185 38.859205 220 0 0 33.063029 38.87464 221 0 0 32.960794 38.781189 222 0 0 33.074026 38.889012 223 0 0 32.967842 38.813784 224 0 0 32.918825 38.786421 225 0 0 32.989176 38.832846 226 0 0 32.991126 38.811462 227 0 0 32.926422 38.774384 228 0 0 32.890468 38.752428 229 0 0 32.897537 38.789535 230 0 0 32.97119 38.829022 231 0 0 32.876088 38.748097 232 0 0 32.976699 38.85726 233 0 0 32.950492 38.841363 234 0 0 32.91384 38.805206 235 0 0 32.945044 38.853031 236 0 0 32.945146 38.837737 237 0 0 32.868877 38.777696 238 0 0 32.985886 38.856607 239 0 0 32.922403 38.813819 240 0 0 32.885764 38.786507 241 0 0 32.982197 38.843464 242 0 0 32.880952 38.817843 243 0 0 32.814101 38.772344 244 0 0 32.860441 38.809646 245 0 0 32.767845 38.737637 246 0 0 32.680741 38.686264 247 0 0 32.719789 38.672785 248 0 0 32.62037 38.632407 249 0 0 32.768809 38.731758 250 0 0 32.572612 38.583398 251 0 0 32.482509 38.53547 252 0 0 32.601353 38.592401 253 0 0 32.616832 38.631331 254 0 0 32.624717 38.649873 255 0 0 32.492356 38.541082 256 0 0 32.551592 38.580821 257 0 0 32.459535 38.554527 258 0 0 32.310985 38.436558 259 0 0 32.527531 38.595841 260 0 0 32.318048 38.477524 261 0 0 32.583888 38.624206 262 0 0 32.416433 38.493931 263 0 0 32.374318 38.493314 264 0 0 32.193673 38.384287 265 0 0 32.354514 38.494766 266 0 0 32.237144 38.458063 267 0 0 32.435541 38.545501 268 0 0 32.030311 38.307304 269 0 0 32.294501 38.483016 270 0 0 32.127873 38.369617 271 0 0 32.084537 38.317995 272 0 0 32.083717 38.320238 273 0 0 32.15522 38.366941 274 0 0 32.123116 38.336963 275 0 0 31.931103 38.207731 276 0 0 32.225462 38.413587 277 0 0 31.6392 37.979007 278 0 0 31.963374 38.210748 279 0 0 31.779994 38.103611 280 0 0 31.906416 38.191132 281 0 0 31.73423 38.09414 282 0 0 31.752365 38.085046 283 0 0 31.82707 38.138787 284 0 0 31.57768 37.983379 285 0 0 31.589664 38.01029 286 0 0 31.885968 38.134517 287 0 0 31.776926 38.082634 288 0 0 31.845866 38.182442 289 0 0 31.761594 38.10681 290 0 0 31.76168 38.089517 291 0 0 31.646677 37.979876 292 0 0 31.840804 38.124145 293 0 0 31.935456 38.227194 294 0 0 31.849912 38.180164 295 0 0 32.018051 38.285048 296 0 0 31.983341 38.244177 297 0 0 32.072951 38.310911 298 0 0 31.866407 38.148545 299 0 0 32.081459 38.375479 300 0 0 31.970302 38.265916 301 0 0 31.993737 38.245303 302 0 0 32.155851 38.296454 303 0 0 31.502726 37.882043 304 0 0 31.829882 38.186719 305 0 0 31.896119 38.135654 306 0 0 31.642019 38.084898 307 0 0 31.638066 37.982679 308 0 0 31.895327 38.193977 309 0 0 31.817537 38.119063 310 0 0 31.749499 38.107771 311 0 0 31.636052 37.969614 312 0 0 31.610362 37.9392 313 0 0 31.823659 38.150135 314 0 0 31.406728 37.795107 315 0 0 31.448494 37.829635 316 0 0 31.581743 37.939419 317 0 0 31.816112 38.112668 318 0 0 31.296774 37.789247 319 0 0 31.179191 37.685292 320 0 0 31.117227 37.577982 321 0 0 31.517167 37.980329 322 0 0 31.553916 37.958759 323 0 0 31.663082 37.943847 324 0 0 31.488722 37.897661 325 0 0 31.557895 37.989912 326 0 0 31.716621 38.035422 327 0 0 31.871492 38.269325 328 0 0 32.186813 38.390372 329 0 0 31.730449 38.039933 330 0 0 31.18662 37.728873 331 0 0 31.450382 37.820611 332 0 0 31.686475 38.032787 333 0 0 31.53913 38.027536 334 0 0 30.901869 37.411215 335 0 0 31.501259 37.784215 336 0 0 31.466125 37.854562 337 0 0 31.814159 38.087512 338 0 0 31.083851 37.732919 339 0 0 30.553691 37.130872 340 0 0 31.060284 37.466903 341 0 0 31.39313 37.829517 342 0 0 31.234568 37.781893 343 0 0 30.37069 37.153736 344 0 0 31.090047 37.744076 345 0 0 30.75 37.434028 346 0 0 30.633136 37.149901 347 0 0 31.039735 37.573951 348 0 0 30.955882 37.651961 349 0 0 30.327869 36.756831 350 0 0 30.306306 36.885886 351 0 0 31.252632 37.817544 352 0 0 31.4125 37.8 353 0 0 31.763889 38.018519 354 0 0 31.47619 38.10582 355 0 0 30.12069 36.988506 356 0 0 27.36 34.96 357 0 0 32.232558 38.635659 358 0 0 31.138889 38 359 0 0 30.961538 36.884615 360 0 0 31.130435 37.42029 361 0 0 33 38.833333 362 0 0 30.352941 37.784314 363 0 0 29.058824 35.823529 364 0 0 29.5625 36.166667 365 0 0 29.071429 36.595238 366 0 0 26.214286 34.119048 367 0 0 26.461538 35.076923 368 0 0 26.4 34.066667 369 0 0 28.555556 35.962963 370 0 0 26.5 33.625 371 0 0 30.875 37.541667 372 0 0 29.875 38.125 373 0 0 31.142857 37.333333 374 0 0 26.428571 35.142857 375 0 0 30.857143 38.333333 376 0 0 35.166667 40.5 377 0 0 34.666667 39.777778 378 0 0 31 37.466667 379 0 0 31.5 37.916667 380 0 0 36 41 381 0 0 33.666667 39.666667 382 0 0 33.666667 39.666667 383 0 0 33.666667 39.666667 384 0 0 31 36 385 0 0 31 36.333333 386 0 0 31 36.333333 387 0 0 31 37.222222 388 0 0 26 31 389 0 0 36 41 390 0 0 35 39.666667 391 0 0 36 41 392 0 0 36 41 393 0 0 28 37 394 0 0 36 41 395 0 0 36 41