## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5276-Z0017-CACGTGGCACATGAT/441525-L5276-Z0017-CACGTGGCACATGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5276-Z0017-CACGTGGCACATGAT/441525-L5276-Z0017-CACGTGGCACATGAT_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 02:56:48 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 999283 999283 148 148089066 148089066 143410525 143410525 133822799 133822799 0 0 0.968407 0.903664 0 0.968407 0.903664 0 444267198 444267198 438153292 438153292 423116052 423116052 396650815 396650815 0.986238 0.952391 0.89282 0.986238 0.952391 0.89282 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 905 0 35.987268 40.99111 1 11433 0 35.980192 40.98598 2 14927 5629 35.991838 40.993231 3 35162 1379 35.94117 40.953488 4 54855 47984 35.977531 40.981633 5 111985 14967 35.989516 40.991194 6 101070 128609 35.92785 40.941705 7 193150 157750 35.960905 40.973393 8 178624 139636 35.978789 40.983248 9 233035 105506 35.845965 40.868475 10 240231 488107 35.824608 40.874063 11 284189 61492 35.858905 40.90557 12 324935 689364 35.368639 40.474497 13 326318 193285 34.038221 39.790536 14 430120 931147 35.803715 40.882214 15 364120 363649 35.638719 40.749427 16 354349 387395 35.547573 40.606477 17 504411 1027160 35.824353 40.855148 18 531502 712107 35.52038 40.615229 19 383220 658740 35.623042 40.717823 20 546134 971201 35.869882 40.910762 21 662156 1365129 35.798907 40.858667 22 353976 533838 35.559367 40.708428 23 1127216 1373476 35.25866 40.511934 24 598898 1209791 35.30367 40.534828 25 549475 509839 35.301154 40.530454 26 1831860 2550404 35.234757 40.484514 27 383247 950091 35.255782 40.501768 28 977007 439313 35.283798 40.519785 29 2557757 5134158 35.278416 40.515852 30 875760 46702 35.268566 40.508571 31 2523529 988815 35.266102 40.504262 32 1840790 5452502 35.273428 40.508319 33 937938 142031 35.271925 40.508241 34 2697857 3141367 35.267904 40.505151 35 2469780 3925658 35.289708 40.519994 36 122477145 2402048 35.314999 40.536316 37 0 4416445 35.308999 40.536592 38 0 489558 35.306518 40.53414 39 0 5460111 35.311145 40.536322 40 0 3 35.303801 40.529812 41 0 396650812 35.292088 40.521835 42 0 0 35.284562 40.517325 43 0 0 35.291425 40.521221 44 0 0 35.297531 40.52562 45 0 0 35.305174 40.530749 46 0 0 35.295717 40.524785 47 0 0 35.291529 40.521854 48 0 0 35.287983 40.51915 49 0 0 35.283603 40.516948 50 0 0 35.278255 40.512677 51 0 0 35.280311 40.513636 52 0 0 35.273957 40.509048 53 0 0 35.264294 40.503609 54 0 0 35.260168 40.499514 55 0 0 35.255382 40.497626 56 0 0 35.242261 40.488502 57 0 0 35.24308 40.488118 58 0 0 35.229599 40.478253 59 0 0 35.222167 40.47149 60 0 0 35.206353 40.460031 61 0 0 35.186215 40.445902 62 0 0 35.155995 40.422548 63 0 0 35.132959 40.405427 64 0 0 35.107725 40.386036 65 0 0 35.075346 40.362285 66 0 0 35.04138 40.337196 67 0 0 34.996178 40.304983 68 0 0 34.960618 40.277791 69 0 0 34.910234 40.239326 70 0 0 34.8535 40.192939 71 0 0 34.78957 40.144911 72 0 0 34.726923 40.093285 73 0 0 34.660835 40.040259 74 0 0 34.596929 39.987984 75 0 0 34.520729 39.927688 76 0 0 34.447315 39.874159 77 0 0 34.371782 39.815852 78 0 0 34.30553 39.761647 79 0 0 34.226112 39.70118 80 0 0 34.169145 39.653254 81 0 0 34.099503 39.597552 82 0 0 34.042346 39.551004 83 0 0 33.980682 39.501069 84 0 0 33.93612 39.467236 85 0 0 33.873398 39.414799 86 0 0 33.841117 39.388349 87 0 0 33.79033 39.348181 88 0 0 33.735705 39.301735 89 0 0 33.696152 39.269353 90 0 0 33.651419 39.228872 91 0 0 33.606981 39.189046 92 0 0 33.579059 39.164536 93 0 0 33.557638 39.144244 94 0 0 33.533691 39.124264 95 0 0 33.509261 39.103002 96 0 0 33.499664 39.092362 97 0 0 33.483775 39.077816 98 0 0 33.484457 39.078869 99 0 0 33.487449 39.078354 100 0 0 33.498071 39.085883 101 0 0 33.529712 39.111536 102 0 0 33.543141 39.120129 103 0 0 33.57019 39.140322 104 0 0 33.572497 39.142025 105 0 0 33.572089 39.136423 106 0 0 33.575552 39.138718 107 0 0 33.562593 39.124781 108 0 0 33.548194 39.110749 109 0 0 33.522628 39.095438 110 0 0 33.498373 39.075494 111 0 0 33.451826 39.037348 112 0 0 33.410319 39.000796 113 0 0 33.354152 38.953774 114 0 0 33.307948 38.918486 115 0 0 33.259916 38.878034 116 0 0 33.236201 38.860515 117 0 0 33.211126 38.839722 118 0 0 33.210952 38.843509 119 0 0 33.200052 38.837997 120 0 0 33.20861 38.844966 121 0 0 33.214547 38.849467 122 0 0 33.211013 38.844229 123 0 0 33.223383 38.853903 124 0 0 33.224164 38.85515 125 0 0 33.232664 38.857594 126 0 0 33.235531 38.855793 127 0 0 33.232975 38.849559 128 0 0 33.225227 38.838629 129 0 0 33.203612 38.821293 130 0 0 33.173781 38.797159 131 0 0 33.159392 38.788378 132 0 0 33.137434 38.767444 133 0 0 33.131985 38.763563 134 0 0 33.134704 38.765701 135 0 0 33.1395 38.767282 136 0 0 33.116559 38.748936 137 0 0 33.118089 38.748213 138 0 0 33.135783 38.766177 139 0 0 33.14156 38.771026 140 0 0 33.156586 38.781955 141 0 0 33.176694 38.799816 142 0 0 33.189727 38.808844 143 0 0 33.206995 38.822867 144 0 0 33.176211 38.798476 145 0 0 33.170158 38.791768 146 0 0 33.136881 38.763146 147 0 0 33.117711 38.745211 148 0 0 33.098935 38.726755 149 0 0 33.04809 38.684817 150 0 0 33.033946 38.670938 151 0 0 32.979608 38.631067 152 0 0 32.970196 38.62257 153 0 0 32.963512 38.620379 154 0 0 32.963604 38.618944 155 0 0 32.958028 38.615214 156 0 0 32.963984 38.624039 157 0 0 32.98971 38.644394 158 0 0 32.996667 38.643462 159 0 0 33.042041 38.681528 160 0 0 33.047748 38.688457 161 0 0 33.08122 38.714086 162 0 0 33.101997 38.732753 163 0 0 33.114143 38.743 164 0 0 33.118289 38.744627 165 0 0 33.12713 38.753531 166 0 0 33.130119 38.751855 167 0 0 33.096537 38.721924 168 0 0 33.057915 38.69191 169 0 0 33.028842 38.66551 170 0 0 32.990354 38.628847 171 0 0 32.95641 38.610741 172 0 0 32.933146 38.590991 173 0 0 32.934052 38.590395 174 0 0 32.950162 38.607234 175 0 0 32.957231 38.613597 176 0 0 32.964085 38.623477 177 0 0 32.980036 38.64142 178 0 0 33.022675 38.674575 179 0 0 33.047725 38.695136 180 0 0 33.039553 38.691277 181 0 0 33.083711 38.728397 182 0 0 33.107135 38.750701 183 0 0 33.149573 38.787163 184 0 0 33.165851 38.79929 185 0 0 33.203646 38.831454 186 0 0 33.210089 38.83848 187 0 0 33.217505 38.84457 188 0 0 33.205131 38.840828 189 0 0 33.205456 38.836739 190 0 0 33.195424 38.834596 191 0 0 33.17608 38.819493 192 0 0 33.147477 38.800293 193 0 0 33.121519 38.782371 194 0 0 33.108262 38.780138 195 0 0 33.066412 38.753092 196 0 0 33.054475 38.749265 197 0 0 33.037439 38.7369 198 0 0 33.028138 38.734994 199 0 0 33.024624 38.740941 200 0 0 32.999492 38.724966 201 0 0 33.000744 38.734002 202 0 0 32.981713 38.725185 203 0 0 32.992192 38.73273 204 0 0 32.944747 38.704655 205 0 0 32.923064 38.687468 206 0 0 32.893875 38.683518 207 0 0 32.910505 38.695319 208 0 0 32.841184 38.646064 209 0 0 32.837121 38.649311 210 0 0 32.79112 38.616987 211 0 0 32.778235 38.609961 212 0 0 32.770358 38.606872 213 0 0 32.720624 38.574574 214 0 0 32.689282 38.552935 215 0 0 32.626545 38.512815 216 0 0 32.635122 38.528373 217 0 0 32.624647 38.520175 218 0 0 32.654607 38.543314 219 0 0 32.582931 38.492871 220 0 0 32.554419 38.475738 221 0 0 32.495887 38.434855 222 0 0 32.478979 38.429203 223 0 0 32.456513 38.419203 224 0 0 32.430218 38.396027 225 0 0 32.447719 38.415729 226 0 0 32.3692 38.358693 227 0 0 32.344349 38.338723 228 0 0 32.342809 38.336981 229 0 0 32.265046 38.297441 230 0 0 32.281269 38.301743 231 0 0 32.209887 38.25096 232 0 0 32.224136 38.253416 233 0 0 32.166651 38.225509 234 0 0 32.141833 38.21193 235 0 0 32.093743 38.188037 236 0 0 32.129535 38.203531 237 0 0 32.043785 38.155981 238 0 0 32.01115 38.150387 239 0 0 32.014826 38.128863 240 0 0 31.916698 38.072068 241 0 0 31.997226 38.133361 242 0 0 31.939087 38.085998 243 0 0 31.872598 38.046902 244 0 0 31.82009 38.005655 245 0 0 31.773618 37.968848 246 0 0 31.725462 37.964832 247 0 0 31.747822 37.958341 248 0 0 31.723645 37.955091 249 0 0 31.731252 37.938876 250 0 0 31.62255 37.879261 251 0 0 31.62468 37.885383 252 0 0 31.586948 37.884893 253 0 0 31.593404 37.877347 254 0 0 31.512511 37.820231 255 0 0 31.430094 37.777724 256 0 0 31.475239 37.778152 257 0 0 31.441625 37.767449 258 0 0 31.299703 37.687644 259 0 0 31.257878 37.653611 260 0 0 31.243777 37.663616 261 0 0 31.273392 37.662802 262 0 0 31.224874 37.637396 263 0 0 31.269801 37.67461 264 0 0 31.000661 37.477385 265 0 0 31.13277 37.56769 266 0 0 31.086268 37.551911 267 0 0 30.976989 37.458468 268 0 0 30.89086 37.418719 269 0 0 30.868759 37.405965 270 0 0 30.771193 37.349819 271 0 0 30.685637 37.28894 272 0 0 30.686622 37.288304 273 0 0 30.621101 37.239714 274 0 0 30.50548 37.177729 275 0 0 30.468468 37.160568 276 0 0 30.323172 37.033352 277 0 0 30.417793 37.111407 278 0 0 30.137447 36.904957 279 0 0 30.113369 36.891494 280 0 0 30.332369 37.06891 281 0 0 30.022122 36.845429 282 0 0 30.029205 36.858937 283 0 0 29.885085 36.713496 284 0 0 29.842597 36.717452 285 0 0 29.813959 36.696644 286 0 0 29.831068 36.706728 287 0 0 29.786435 36.660174 288 0 0 29.51495 36.468297 289 0 0 29.644868 36.592383 290 0 0 29.4018 36.389033 291 0 0 29.406247 36.432505 292 0 0 29.382996 36.428273 293 0 0 29.251281 36.299662 294 0 0 29.273905 36.36204 295 0 0 28.991299 36.091365 296 0 0 29.233433 36.314054 297 0 0 29.101475 36.214905 298 0 0 29.070832 36.181153 299 0 0 28.970962 36.120646 300 0 0 28.940307 36.048885 301 0 0 28.921786 36.094615 302 0 0 28.806818 35.972039 303 0 0 28.882288 36.005329 304 0 0 28.764472 35.973316 305 0 0 28.679229 35.908268 306 0 0 28.598585 35.922113 307 0 0 28.675718 35.884625 308 0 0 28.775463 35.970145 309 0 0 28.580667 35.828444 310 0 0 28.602278 35.885936 311 0 0 28.448293 35.782646 312 0 0 28.776929 36.035179 313 0 0 28.198765 35.590807 314 0 0 28.496655 35.735691 315 0 0 28.302101 35.629464 316 0 0 28.374008 35.705201 317 0 0 28.59119 35.815287 318 0 0 28.264176 35.59706 319 0 0 28.154073 35.540072 320 0 0 28.390542 35.734148 321 0 0 28.165885 35.475381 322 0 0 28.329684 35.629964 323 0 0 28.150754 35.650634 324 0 0 27.642347 35.141422 325 0 0 27.598022 35.153777 326 0 0 27.872 35.295333 327 0 0 27.663032 35.197746 328 0 0 27.636034 35.1447 329 0 0 27.413165 34.902428 330 0 0 28.468652 35.946186 331 0 0 27.668508 35.216697 332 0 0 27.987552 35.246888 333 0 0 28.291667 35.683642 334 0 0 27.845953 35.470844 335 0 0 27.255452 34.656282 336 0 0 26.979094 34.767712 337 0 0 28.476562 35.895833 338 0 0 27.724444 35.721481 339 0 0 27.575758 35.232323 340 0 0 27.551724 35.116858 341 0 0 29.088608 36.111814 342 0 0 27.089041 34.844749 343 0 0 28.08 35.917333 344 0 0 28.371429 35.933333 345 0 0 26.875 34.677083 346 0 0 27.156627 35.232932 347 0 0 28.369863 35.447489 348 0 0 26 34.141414 349 0 0 27.508197 35 350 0 0 27.886792 35.855346 351 0 0 28.869565 36.355072 352 0 0 27.725 35.575 353 0 0 28.945946 36.531532 354 0 0 26.257143 33.72381 355 0 0 25.529412 33.627451 356 0 0 28.96875 35.25 357 0 0 28.6 35.522222 358 0 0 25.37037 33.851852 359 0 0 28.48 36.186667 360 0 0 26.909091 33.893939 361 0 0 29.526316 37.508772 362 0 0 24.571429 32.357143 363 0 0 27.714286 36.119048 364 0 0 26 32.757576 365 0 0 31.7 37.433333 366 0 0 27.222222 34.185185 367 0 0 27 35.777778 368 0 0 22.333333 31.555556 369 0 0 25.2 33.133333 370 0 0 21.4 29.4 371 0 0 28.4 37.4 372 0 0 22.8 31.933333 373 0 0 25 36.222222 374 0 0 29.666667 36.555556 375 0 0 8 23.333333 376 0 0 31 38 377 0 0 29 33 378 0 0 30 35.333333 379 0 0 35 39.666667 380 0 0 31 36.666667 381 0 0 7 23 382 0 0 29 35 383 0 0 31 38 384 0 0 6 13 385 0 0 36 41 386 0 0 36 41 387 0 0 16 27.333333 388 0 0 17 27.333333 389 0 0 36 41