## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5283-Z0027-CACTGTCAGCCAGAT/441525-L5283-Z0027-CACTGTCAGCCAGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5283-Z0027-CACTGTCAGCCAGAT/441525-L5283-Z0027-CACTGTCAGCCAGAT_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 02:54:44 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 1001067 1001067 171 171334243 171334243 166653894 166653894 157095640 157095640 0 0 0.972683 0.916896 0 0.972683 0.916896 0 514002729 514002729 507911862 507911862 492906620 492906620 466881016 466881016 0.98815 0.958957 0.908324 0.98815 0.958957 0.908324 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 964 0 35.989184 40.992167 1 12946 1 35.981597 40.987662 2 15585 5907 35.992981 40.99436 3 37685 1485 35.983281 40.986521 4 58271 52778 35.989838 40.991988 5 116320 15274 35.994394 40.995427 6 99938 135886 35.973919 40.979603 7 196910 164162 35.978803 40.9857 8 172524 147220 35.985998 40.988593 9 232477 106351 35.939213 40.948908 10 239394 488032 35.912359 40.940918 11 282984 63261 35.947035 40.962301 12 326621 676392 35.582631 40.650571 13 323535 194681 34.671974 40.179951 14 438243 925894 35.905816 40.944888 15 362627 365116 35.702529 40.79819 16 353367 373259 35.75068 40.779452 17 497160 1020014 35.905477 40.922371 18 536307 698581 35.726755 40.781868 19 376491 656573 35.816778 40.866219 20 551502 948987 35.937966 40.958077 21 656834 1355669 35.862103 40.901857 22 356021 533127 35.665704 40.776536 23 1164511 1387732 35.437201 40.625695 24 596576 1212164 35.475696 40.646258 25 544930 505614 35.454227 40.633617 26 1862591 2627699 35.412906 40.602993 27 366286 950944 35.436984 40.622874 28 955471 414060 35.450155 40.631046 29 2503532 5069246 35.440852 40.624063 30 831672 50429 35.431055 40.616959 31 2503192 996340 35.429735 40.614507 32 1821348 5309402 35.429121 40.612976 33 929074 146596 35.427288 40.613509 34 2659893 3049402 35.417879 40.60707 35 2488323 3813507 35.436588 40.619934 36 145862138 2465963 35.455194 40.632355 37 0 4300686 35.449177 40.628956 38 0 546105 35.43973 40.624167 39 0 5347174 35.443029 40.623355 40 0 6 35.433552 40.6177 41 0 466881010 35.419035 40.609148 42 0 0 35.415812 40.605902 43 0 0 35.422578 40.608776 44 0 0 35.433274 40.617589 45 0 0 35.433858 40.617369 46 0 0 35.426885 40.61225 47 0 0 35.418004 40.606553 48 0 0 35.412155 40.603102 49 0 0 35.408269 40.599866 50 0 0 35.408475 40.600164 51 0 0 35.410293 40.600932 52 0 0 35.4044 40.596829 53 0 0 35.397014 40.592827 54 0 0 35.393065 40.590072 55 0 0 35.39042 40.587419 56 0 0 35.386464 40.585483 57 0 0 35.381957 40.582742 58 0 0 35.380523 40.579374 59 0 0 35.366944 40.569847 60 0 0 35.355392 40.560899 61 0 0 35.339421 40.550784 62 0 0 35.327934 40.540848 63 0 0 35.310159 40.52685 64 0 0 35.290315 40.513353 65 0 0 35.265602 40.495268 66 0 0 35.241667 40.476776 67 0 0 35.221911 40.463481 68 0 0 35.191206 40.440709 69 0 0 35.158762 40.415121 70 0 0 35.120171 40.385954 71 0 0 35.08582 40.358509 72 0 0 35.038486 40.321255 73 0 0 34.997629 40.288566 74 0 0 34.961665 40.257702 75 0 0 34.905165 40.215815 76 0 0 34.866496 40.185971 77 0 0 34.817112 40.149301 78 0 0 34.769028 40.110274 79 0 0 34.724537 40.077151 80 0 0 34.684255 40.044215 81 0 0 34.645849 40.014003 82 0 0 34.609227 39.98321 83 0 0 34.575318 39.956759 84 0 0 34.543821 39.93161 85 0 0 34.519979 39.912168 86 0 0 34.4923 39.890604 87 0 0 34.474264 39.875661 88 0 0 34.441309 39.848839 89 0 0 34.408547 39.821834 90 0 0 34.386487 39.800883 91 0 0 34.360371 39.780182 92 0 0 34.337384 39.758656 93 0 0 34.324142 39.746227 94 0 0 34.292444 39.720046 95 0 0 34.278719 39.707928 96 0 0 34.261509 39.695343 97 0 0 34.24405 39.679482 98 0 0 34.245311 39.681692 99 0 0 34.245417 39.67926 100 0 0 34.245357 39.680324 101 0 0 34.262287 39.692726 102 0 0 34.265838 39.695419 103 0 0 34.286267 39.709506 104 0 0 34.299964 39.720312 105 0 0 34.301558 39.719588 106 0 0 34.305275 39.721609 107 0 0 34.316594 39.727456 108 0 0 34.30097 39.714434 109 0 0 34.297163 39.714527 110 0 0 34.285168 39.704413 111 0 0 34.253492 39.678428 112 0 0 34.234447 39.663759 113 0 0 34.193141 39.628355 114 0 0 34.155315 39.59519 115 0 0 34.114206 39.561853 116 0 0 34.096291 39.549059 117 0 0 34.069689 39.529052 118 0 0 34.060334 39.524199 119 0 0 34.058626 39.525349 120 0 0 34.051696 39.518367 121 0 0 34.054149 39.524492 122 0 0 34.062205 39.526607 123 0 0 34.058476 39.520825 124 0 0 34.043539 39.510674 125 0 0 34.063316 39.521589 126 0 0 34.056522 39.512041 127 0 0 34.053182 39.509742 128 0 0 34.04594 39.50014 129 0 0 34.029476 39.488329 130 0 0 34.012417 39.474678 131 0 0 33.992573 39.458225 132 0 0 33.986059 39.453268 133 0 0 33.975314 39.443263 134 0 0 33.964855 39.433495 135 0 0 33.959063 39.424896 136 0 0 33.935337 39.407353 137 0 0 33.926642 39.400564 138 0 0 33.914868 39.392577 139 0 0 33.914709 39.393533 140 0 0 33.921403 39.40098 141 0 0 33.930588 39.407148 142 0 0 33.937531 39.413714 143 0 0 33.936868 39.411533 144 0 0 33.910591 39.390726 145 0 0 33.893409 39.375178 146 0 0 33.86931 39.353842 147 0 0 33.835969 39.323859 148 0 0 33.797705 39.290443 149 0 0 33.772109 39.270571 150 0 0 33.717881 39.227268 151 0 0 33.703439 39.216069 152 0 0 33.664896 39.188435 153 0 0 33.647307 39.174945 154 0 0 33.642083 39.168884 155 0 0 33.640569 39.168384 156 0 0 33.616432 39.145093 157 0 0 33.613382 39.138478 158 0 0 33.615241 39.139853 159 0 0 33.610964 39.137362 160 0 0 33.621279 39.143212 161 0 0 33.64392 39.162663 162 0 0 33.641971 39.161618 163 0 0 33.651304 39.169502 164 0 0 33.632997 39.152352 165 0 0 33.624033 39.144368 166 0 0 33.59246 39.119075 167 0 0 33.555147 39.085041 168 0 0 33.502663 39.036478 169 0 0 33.468808 39.006357 170 0 0 33.420129 38.963859 171 0 0 33.369727 38.923516 172 0 0 33.35633 38.915621 173 0 0 33.320951 38.886023 174 0 0 33.320589 38.886375 175 0 0 33.31764 38.884642 176 0 0 33.318844 38.885101 177 0 0 33.333259 38.896732 178 0 0 33.341724 38.901524 179 0 0 33.365189 38.920742 180 0 0 33.379351 38.936205 181 0 0 33.398195 38.951824 182 0 0 33.450551 38.99503 183 0 0 33.482663 39.023501 184 0 0 33.506988 39.040294 185 0 0 33.528434 39.058353 186 0 0 33.557835 39.081098 187 0 0 33.579428 39.098148 188 0 0 33.592007 39.109432 189 0 0 33.58455 39.107059 190 0 0 33.592888 39.108191 191 0 0 33.577679 39.102198 192 0 0 33.568191 39.097156 193 0 0 33.554908 39.090686 194 0 0 33.54033 39.085509 195 0 0 33.513064 39.066248 196 0 0 33.509789 39.07039 197 0 0 33.511572 39.077777 198 0 0 33.508585 39.07986 199 0 0 33.483014 39.065664 200 0 0 33.47587 39.067351 201 0 0 33.455623 39.055914 202 0 0 33.431411 39.042841 203 0 0 33.440008 39.055831 204 0 0 33.426402 39.051651 205 0 0 33.396683 39.032161 206 0 0 33.374975 39.020962 207 0 0 33.34211 39.006709 208 0 0 33.359853 39.01967 209 0 0 33.323734 39.002919 210 0 0 33.296189 38.982268 211 0 0 33.255053 38.955285 212 0 0 33.258681 38.962101 213 0 0 33.257275 38.963366 214 0 0 33.220535 38.939923 215 0 0 33.209973 38.939942 216 0 0 33.185688 38.93029 217 0 0 33.174859 38.919821 218 0 0 33.153638 38.905985 219 0 0 33.141188 38.903972 220 0 0 33.098412 38.871721 221 0 0 33.087566 38.866445 222 0 0 33.084014 38.866718 223 0 0 33.026765 38.825464 224 0 0 33.014379 38.821621 225 0 0 32.999979 38.810651 226 0 0 32.951702 38.783691 227 0 0 32.937538 38.769877 228 0 0 32.910605 38.752735 229 0 0 32.91444 38.759176 230 0 0 32.871069 38.721506 231 0 0 32.83365 38.712589 232 0 0 32.838658 38.714621 233 0 0 32.793489 38.685913 234 0 0 32.768436 38.67583 235 0 0 32.713929 38.636433 236 0 0 32.717198 38.638526 237 0 0 32.698421 38.625402 238 0 0 32.647992 38.588849 239 0 0 32.584809 38.553367 240 0 0 32.604946 38.566179 241 0 0 32.554213 38.54364 242 0 0 32.543098 38.530337 243 0 0 32.525063 38.530547 244 0 0 32.471451 38.480898 245 0 0 32.432318 38.46193 246 0 0 32.420889 38.461201 247 0 0 32.390159 38.427497 248 0 0 32.334121 38.404559 249 0 0 32.293613 38.373412 250 0 0 32.30655 38.396965 251 0 0 32.273989 38.358721 252 0 0 32.244576 38.348598 253 0 0 32.214007 38.332037 254 0 0 32.149636 38.280733 255 0 0 32.163905 38.291058 256 0 0 32.129192 38.264689 257 0 0 32.096629 38.247014 258 0 0 32.011513 38.1954 259 0 0 32.011873 38.19778 260 0 0 31.942273 38.152377 261 0 0 31.961775 38.16782 262 0 0 31.886942 38.122726 263 0 0 31.850623 38.099221 264 0 0 31.832225 38.099813 265 0 0 31.750211 38.029325 266 0 0 31.668279 37.982712 267 0 0 31.621398 37.945486 268 0 0 31.524493 37.895532 269 0 0 31.516757 37.877853 270 0 0 31.440432 37.835337 271 0 0 31.445262 37.830688 272 0 0 31.397087 37.80823 273 0 0 31.324586 37.762152 274 0 0 31.229894 37.696597 275 0 0 31.193709 37.681472 276 0 0 31.104147 37.605179 277 0 0 31.015437 37.543631 278 0 0 30.99563 37.536957 279 0 0 30.912139 37.479899 280 0 0 30.828323 37.439352 281 0 0 30.786992 37.405387 282 0 0 30.713512 37.348626 283 0 0 30.67079 37.317528 284 0 0 30.575336 37.25537 285 0 0 30.477885 37.198725 286 0 0 30.475453 37.170252 287 0 0 30.404778 37.11064 288 0 0 30.379912 37.109753 289 0 0 30.308773 37.05079 290 0 0 30.178596 36.954751 291 0 0 30.12532 36.933913 292 0 0 30.011518 36.85252 293 0 0 29.986144 36.836622 294 0 0 30.003809 36.861203 295 0 0 29.871449 36.757606 296 0 0 29.780914 36.695131 297 0 0 29.752686 36.691502 298 0 0 29.680668 36.607968 299 0 0 29.617792 36.573896 300 0 0 29.520452 36.521376 301 0 0 29.517806 36.538742 302 0 0 29.495873 36.507396 303 0 0 29.3465 36.39456 304 0 0 29.440695 36.447573 305 0 0 29.286006 36.379199 306 0 0 29.348887 36.38618 307 0 0 29.241091 36.311063 308 0 0 29.276887 36.349918 309 0 0 29.136315 36.246872 310 0 0 29.003004 36.14999 311 0 0 29.075528 36.206816 312 0 0 29.099253 36.169721 313 0 0 29.090307 36.170984 314 0 0 29.12188 36.241657 315 0 0 29.027796 36.159826 316 0 0 29.027839 36.130245 317 0 0 28.854479 36.038541 318 0 0 28.88007 36.066434 319 0 0 28.862836 36.027408 320 0 0 28.68516 35.899642 321 0 0 28.69151 35.910293 322 0 0 28.782738 35.960413 323 0 0 28.808404 35.990124 324 0 0 28.689818 35.895817 325 0 0 28.731157 35.887123 326 0 0 28.563169 35.766516 327 0 0 28.916623 36.067433 328 0 0 28.536885 35.851678 329 0 0 28.358069 35.710089 330 0 0 28.43759 35.679579 331 0 0 28.535474 35.826001 332 0 0 28.716563 35.949365 333 0 0 28.56588 35.810718 334 0 0 28.018202 35.467917 335 0 0 28.635177 35.97369 336 0 0 28.648045 35.896881 337 0 0 28.878884 36.068792 338 0 0 28.120536 35.397917 339 0 0 28.241206 35.697487 340 0 0 28.74442 36.002976 341 0 0 28.326683 35.54655 342 0 0 27.680339 35.086752 343 0 0 28.291057 35.634688 344 0 0 27.222836 34.815838 345 0 0 27.904366 35.188496 346 0 0 28.918114 36.105873 347 0 0 28.938953 36.281977 348 0 0 27.932886 35.542506 349 0 0 28.637066 36.096525 350 0 0 29.102564 36.222222 351 0 0 28.478261 35.731079 352 0 0 27.835165 35.593407 353 0 0 27.746988 35.299197 354 0 0 27.823129 35.369615 355 0 0 30.436975 37.252101 356 0 0 29.912621 36.627832 357 0 0 25.89011 34.168498 358 0 0 27.291139 34.936709 359 0 0 27.472222 35.152778 360 0 0 26.916667 34.822222 361 0 0 30.923077 37.801282 362 0 0 28.333333 35.822222 363 0 0 28.95122 36.471545 364 0 0 29.894737 36.894737 365 0 0 28.918919 36.432432 366 0 0 26.914286 34.761905 367 0 0 27.6 35.344444 368 0 0 26.259259 34.580247 369 0 0 28.56 35.613333 370 0 0 28.909091 36.454545 371 0 0 29.454545 36.757576 372 0 0 30.15 37.466667 373 0 0 28.333333 36.092593 374 0 0 28.866667 35.177778 375 0 0 30.153846 36.25641 376 0 0 27.818182 35.363636 377 0 0 30.1 36.3 378 0 0 27.5 35.944444 379 0 0 33.6 39.866667 380 0 0 31.75 38 381 0 0 25.333333 34.222222 382 0 0 26 34.444444 383 0 0 32.5 38.5 384 0 0 33 37.666667 385 0 0 29 37 386 0 0 26 33