## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5287-Z0032-CTCTGTATTGCAGAT/441525-L5287-Z0032-CTCTGTATTGCAGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5287-Z0032-CTCTGTATTGCAGAT/441525-L5287-Z0032-CTCTGTATTGCAGAT_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 02:54:32 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 998320 998320 132 131878649 131878649 127234330 127234330 118068356 118068356 0 0 0.964783 0.89528 0 0.964783 0.89528 0 395635947 395635947 389477258 389477258 375020438 375020438 350488761 350488761 0.984433 0.947893 0.885887 0.984433 0.947893 0.885887 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 697 0 35.994327 40.995804 1 9038 0 35.987396 40.991559 2 11480 3545 35.994361 40.995352 3 28292 1028 35.982393 40.985705 4 49070 38723 35.99157 40.993253 5 93698 14261 35.99472 40.995743 6 106721 101817 35.97614 40.98072 7 170237 134570 35.978257 40.984956 8 190090 136068 35.98772 40.990171 9 219544 90547 35.956034 40.963728 10 230163 480860 35.892278 40.933826 11 273997 50938 35.929536 40.948398 12 329704 661272 35.223792 40.347459 13 343962 195821 33.741837 39.597263 14 432922 949602 35.88341 40.929875 15 355009 349850 35.781564 40.845981 16 378671 447332 35.73031 40.759584 17 511609 1107433 35.867983 40.88587 18 537559 688269 35.74479 40.79046 19 371856 706753 35.75014 40.811653 20 489712 1024673 35.904812 40.936151 21 637287 1308085 35.856743 40.899342 22 314840 568840 35.633612 40.758314 23 1011151 1160073 35.377139 40.585828 24 555452 1118780 35.382422 40.588106 25 549141 479691 35.399976 40.597448 26 1786212 2497213 35.341426 40.555144 27 341018 840066 35.359131 40.56808 28 961414 359250 35.388044 40.588168 29 2519747 5100149 35.390067 40.588227 30 750154 39525 35.382937 40.581447 31 2363764 769520 35.382771 40.580197 32 1514714 5504985 35.3781 40.575512 33 839490 114213 35.373968 40.575551 34 2449862 2452606 35.371835 40.573564 35 2255412 3930126 35.382052 40.581332 36 107894960 1933937 35.40933 40.598239 37 0 4375394 35.413972 40.604273 38 0 372202 35.407576 40.599011 39 0 5039169 35.403862 40.595089 40 0 1 35.399896 40.592169 41 0 350488760 35.389374 40.584839 42 0 0 35.380203 40.57927 43 0 0 35.382712 40.580317 44 0 0 35.395711 40.588933 45 0 0 35.399893 40.592314 46 0 0 35.391214 40.586146 47 0 0 35.38646 40.583616 48 0 0 35.376923 40.576338 49 0 0 35.384059 40.580664 50 0 0 35.37634 40.574381 51 0 0 35.366124 40.567865 52 0 0 35.362656 40.565544 53 0 0 35.349122 40.557504 54 0 0 35.338933 40.549941 55 0 0 35.327117 40.540409 56 0 0 35.306319 40.527434 57 0 0 35.288028 40.512533 58 0 0 35.265131 40.495584 59 0 0 35.234667 40.473585 60 0 0 35.188807 40.440383 61 0 0 35.14136 40.404437 62 0 0 35.088475 40.363567 63 0 0 35.028122 40.318294 64 0 0 34.960448 40.265772 65 0 0 34.891603 40.214559 66 0 0 34.810378 40.154083 67 0 0 34.715952 40.084942 68 0 0 34.618255 40.011544 69 0 0 34.508902 39.928991 70 0 0 34.398444 39.843123 71 0 0 34.277616 39.745236 72 0 0 34.163721 39.653331 73 0 0 34.048863 39.562973 74 0 0 33.92519 39.463106 75 0 0 33.815307 39.379634 76 0 0 33.713773 39.299445 77 0 0 33.613882 39.223756 78 0 0 33.536935 39.166058 79 0 0 33.450851 39.100117 80 0 0 33.380044 39.04042 81 0 0 33.316494 38.990738 82 0 0 33.261259 38.941395 83 0 0 33.212646 38.901243 84 0 0 33.173286 38.868855 85 0 0 33.129051 38.835077 86 0 0 33.097151 38.803632 87 0 0 33.059274 38.771924 88 0 0 33.006949 38.726367 89 0 0 32.971556 38.699352 90 0 0 32.916992 38.64924 91 0 0 32.87926 38.61433 92 0 0 32.857236 38.591629 93 0 0 32.811164 38.556187 94 0 0 32.782931 38.530174 95 0 0 32.768655 38.51808 96 0 0 32.756252 38.505389 97 0 0 32.756762 38.50485 98 0 0 32.762462 38.505462 99 0 0 32.792754 38.532124 100 0 0 32.825147 38.557448 101 0 0 32.872837 38.594113 102 0 0 32.922891 38.635025 103 0 0 32.956479 38.657975 104 0 0 32.9908 38.681865 105 0 0 32.98468 38.674069 106 0 0 32.971056 38.659772 107 0 0 32.952639 38.642044 108 0 0 32.932556 38.624637 109 0 0 32.895398 38.596148 110 0 0 32.845306 38.559567 111 0 0 32.794181 38.51672 112 0 0 32.734373 38.468761 113 0 0 32.662383 38.410316 114 0 0 32.59855 38.361466 115 0 0 32.528849 38.304967 116 0 0 32.507709 38.290385 117 0 0 32.482749 38.271674 118 0 0 32.482439 38.269897 119 0 0 32.48546 38.276292 120 0 0 32.486718 38.275389 121 0 0 32.498723 38.281215 122 0 0 32.510725 38.290098 123 0 0 32.526798 38.300512 124 0 0 32.531528 38.303449 125 0 0 32.54642 38.312482 126 0 0 32.566839 38.32583 127 0 0 32.553782 38.305411 128 0 0 32.516878 38.276099 129 0 0 32.481614 38.243245 130 0 0 32.43678 38.206195 131 0 0 32.408287 38.184548 132 0 0 32.393781 38.170695 133 0 0 32.381871 38.158545 134 0 0 32.375881 38.155545 135 0 0 32.371942 38.151426 136 0 0 32.370344 38.147902 137 0 0 32.357443 38.141017 138 0 0 32.359646 38.143416 139 0 0 32.377571 38.159082 140 0 0 32.418518 38.189281 141 0 0 32.438439 38.203361 142 0 0 32.431378 38.195029 143 0 0 32.446332 38.210722 144 0 0 32.446029 38.211554 145 0 0 32.440522 38.204408 146 0 0 32.420464 38.188206 147 0 0 32.387461 38.154601 148 0 0 32.371502 38.141291 149 0 0 32.330979 38.106751 150 0 0 32.316709 38.088037 151 0 0 32.269924 38.051882 152 0 0 32.234628 38.026938 153 0 0 32.241847 38.03185 154 0 0 32.265421 38.061364 155 0 0 32.273542 38.064789 156 0 0 32.286951 38.073382 157 0 0 32.33336 38.11793 158 0 0 32.346438 38.123918 159 0 0 32.412415 38.173158 160 0 0 32.484389 38.229212 161 0 0 32.512139 38.250418 162 0 0 32.55292 38.279762 163 0 0 32.58592 38.310541 164 0 0 32.624106 38.339904 165 0 0 32.633562 38.346694 166 0 0 32.644665 38.355771 167 0 0 32.629499 38.343895 168 0 0 32.632728 38.341687 169 0 0 32.638652 38.342213 170 0 0 32.635022 38.336458 171 0 0 32.62999 38.33266 172 0 0 32.619217 38.327449 173 0 0 32.648844 38.356164 174 0 0 32.678111 38.382748 175 0 0 32.659724 38.37208 176 0 0 32.697045 38.403327 177 0 0 32.786506 38.475313 178 0 0 32.841963 38.522257 179 0 0 32.877532 38.555801 180 0 0 32.940692 38.604789 181 0 0 32.934419 38.602835 182 0 0 32.994127 38.655066 183 0 0 33.039653 38.693341 184 0 0 33.04175 38.696327 185 0 0 33.117949 38.752939 186 0 0 33.085697 38.728013 187 0 0 33.135786 38.775523 188 0 0 33.158606 38.797056 189 0 0 33.127383 38.775682 190 0 0 33.165151 38.80224 191 0 0 33.188444 38.816044 192 0 0 33.141095 38.783409 193 0 0 33.156632 38.810521 194 0 0 33.154804 38.808187 195 0 0 33.106903 38.778326 196 0 0 33.122436 38.797398 197 0 0 33.159835 38.831792 198 0 0 33.179157 38.847927 199 0 0 33.157644 38.849599 200 0 0 33.141465 38.834819 201 0 0 33.153845 38.85271 202 0 0 33.167739 38.870186 203 0 0 33.115382 38.8396 204 0 0 33.175 38.888586 205 0 0 33.137279 38.862675 206 0 0 33.145248 38.874694 207 0 0 33.120258 38.854617 208 0 0 33.094247 38.836421 209 0 0 33.075381 38.826576 210 0 0 33.120811 38.851217 211 0 0 33.106766 38.852712 212 0 0 33.053766 38.825206 213 0 0 33.030909 38.80523 214 0 0 33.026536 38.803196 215 0 0 32.951028 38.761529 216 0 0 32.949643 38.762113 217 0 0 32.989937 38.804331 218 0 0 32.985125 38.801156 219 0 0 32.958279 38.753982 220 0 0 32.848495 38.693338 221 0 0 32.848872 38.693007 222 0 0 32.813378 38.673938 223 0 0 32.821027 38.690882 224 0 0 32.794628 38.675084 225 0 0 32.79108 38.66371 226 0 0 32.731829 38.642222 227 0 0 32.771402 38.671644 228 0 0 32.745639 38.636317 229 0 0 32.683174 38.603557 230 0 0 32.673279 38.596 231 0 0 32.656372 38.582966 232 0 0 32.697308 38.629021 233 0 0 32.549376 38.499034 234 0 0 32.625502 38.572019 235 0 0 32.519188 38.491194 236 0 0 32.523771 38.486894 237 0 0 32.458703 38.466764 238 0 0 32.366812 38.390213 239 0 0 32.410163 38.422837 240 0 0 32.379886 38.416417 241 0 0 32.390138 38.407507 242 0 0 32.313297 38.366183 243 0 0 32.214491 38.298798 244 0 0 32.181981 38.280147 245 0 0 32.155506 38.251136 246 0 0 32.193183 38.283941 247 0 0 32.110032 38.24136 248 0 0 32.097247 38.21871 249 0 0 32.02484 38.192029 250 0 0 32.015526 38.160125 251 0 0 31.981753 38.116293 252 0 0 31.949221 38.137845 253 0 0 31.786302 38.009179 254 0 0 31.722762 37.972279 255 0 0 31.769157 38.01614 256 0 0 31.726043 37.967427 257 0 0 31.656878 37.925477 258 0 0 31.61228 37.901526 259 0 0 31.700048 37.98856 260 0 0 31.687895 37.96839 261 0 0 31.552244 37.870563 262 0 0 31.432324 37.795659 263 0 0 31.341135 37.715313 264 0 0 31.414018 37.790446 265 0 0 31.243744 37.690533 266 0 0 31.238482 37.675745 267 0 0 31.228536 37.664255 268 0 0 31.226057 37.640058 269 0 0 31.058118 37.577837 270 0 0 31.109426 37.613842 271 0 0 30.993091 37.545473 272 0 0 31.044014 37.525534 273 0 0 30.883676 37.453854 274 0 0 30.69684 37.323533 275 0 0 30.839065 37.421293 276 0 0 30.699506 37.308426 277 0 0 30.699377 37.371215 278 0 0 30.411652 37.118077 279 0 0 30.381606 37.074188 280 0 0 30.438167 37.135384 281 0 0 30.246108 37.040139 282 0 0 30.314425 37.047337 283 0 0 30.353869 37.071403 284 0 0 30.12062 36.915247 285 0 0 30.213133 36.97616 286 0 0 30.13494 36.919643 287 0 0 30.103516 36.869051 288 0 0 30.05501 36.888266 289 0 0 29.978215 36.827981 290 0 0 29.854229 36.718823 291 0 0 30.069252 36.879905 292 0 0 29.847354 36.700987 293 0 0 29.909613 36.807619 294 0 0 29.637361 36.601385 295 0 0 29.761706 36.678422 296 0 0 29.539403 36.568229 297 0 0 29.584592 36.556539 298 0 0 29.648716 36.578714 299 0 0 29.441294 36.432154 300 0 0 29.411664 36.39884 301 0 0 29.551452 36.476821 302 0 0 29.692861 36.676789 303 0 0 29.534916 36.564804 304 0 0 29.185522 36.346913 305 0 0 29.371042 36.362127 306 0 0 29.31562 36.390231 307 0 0 29.302381 36.33322 308 0 0 29.120201 36.221146 309 0 0 29.301496 36.363509 310 0 0 28.994269 36.100287 311 0 0 29.214724 36.318726 312 0 0 28.891829 36.078304 313 0 0 29.26925 36.310647 314 0 0 29.341139 36.385134 315 0 0 29.287529 36.288299 316 0 0 29.039385 36.265436 317 0 0 28.857718 36.074049 318 0 0 29.50612 36.481881 319 0 0 29.115325 36.210784 320 0 0 28.79258 35.968241 321 0 0 28.857661 36.058024 322 0 0 29.656155 36.580197 323 0 0 29.362416 36.420582 324 0 0 28.942892 36.08303 325 0 0 29.835079 36.571117 326 0 0 29.361032 36.320917 327 0 0 30.040185 36.780526 328 0 0 29.450085 36.536379 329 0 0 28.850277 36.024646 330 0 0 29.52 36.437333 331 0 0 29.104575 36.125635 332 0 0 29.101449 36.160225 333 0 0 29.577236 36.496838 334 0 0 28.932353 35.985294 335 0 0 29.563863 36.354102 336 0 0 29.567944 36.549361 337 0 0 30.225806 36.896505 338 0 0 30.438356 37.12481 339 0 0 30.598985 37.267343 340 0 0 31.138122 37.500921 341 0 0 29.327273 36.177778 342 0 0 29.586667 36.62 343 0 0 30.58209 36.853234 344 0 0 30.181818 37.041322 345 0 0 30.59633 37.547401 346 0 0 30.525773 37.439863 347 0 0 30.494382 36.962547 348 0 0 30.910256 37.820513 349 0 0 29.75 37.098039 350 0 0 30.412698 37.095238 351 0 0 32.1 38.453333 352 0 0 28.547619 36.253968 353 0 0 31.7 37.616667 354 0 0 29.72973 36.306306 355 0 0 30.096774 36.817204 356 0 0 27.807692 34.961538 357 0 0 30.318182 36.878788 358 0 0 28.947368 36.192982 359 0 0 32.3125 38 360 0 0 31.333333 38.111111 361 0 0 26.5 34.566667 362 0 0 25.888889 32.592593 363 0 0 30.285714 36.952381 364 0 0 24.857143 33 365 0 0 32.4 38.666667 366 0 0 30.8 37.933333 367 0 0 27 36.133333 368 0 0 28.5 36.5 369 0 0 31.5 37 370 0 0 25.5 34.5 371 0 0 26 35.083333 372 0 0 20 30.666667 373 0 0 29.5 38 374 0 0 25 33.222222 375 0 0 24.666667 33 376 0 0 36 41 377 0 0 26 31 378 0 0 36 41 379 0 0 30 38.166667 380 0 0 35 40.166667