## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5371-Z0039-CACAACATATCAGAT/441525-L5371-Z0039-CACAACATATCAGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5371-Z0039-CACAACATATCAGAT/441525-L5371-Z0039-CACAACATATCAGAT_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 02:56:39 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 999444 999444 132 132244848 132244848 127100077 127100077 117751951 117751951 0 0 0.961097 0.890409 0 0.961097 0.890409 0 396734544 396734544 389917458 389917458 374851299 374851299 350116601 350116601 0.982817 0.944842 0.882496 0.982817 0.944842 0.882496 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 968 0 35.992647 40.994424 1 12785 0 35.986018 40.990576 2 15290 5151 35.994625 40.995492 3 39617 1505 35.985136 40.988025 4 61169 54833 35.991359 40.993203 5 123107 19868 35.994079 40.995246 6 115188 142939 35.977651 40.981687 7 213345 178723 35.973102 40.981956 8 202604 156738 35.981999 40.984855 9 259206 126270 35.958016 40.964712 10 274243 530178 35.895331 40.935817 11 319100 71462 35.927965 40.947018 12 374191 749476 35.292873 40.403511 13 364279 229226 33.899546 39.697075 14 487631 1046375 35.888543 40.932874 15 393477 404401 35.81883 40.870829 16 400518 452891 35.797177 40.819523 17 533164 1146830 35.896621 40.913894 18 577129 778809 35.759762 40.803853 19 377760 721411 35.743731 40.816141 20 534328 1011751 35.890388 40.930376 21 687132 1442573 35.822023 40.872082 22 332102 560680 35.567639 40.704127 23 1085768 1271498 35.268757 40.503167 24 601200 1248425 35.242052 40.487886 25 548504 474014 35.229919 40.477995 26 1784688 2617861 35.167699 40.432218 27 376565 900283 35.180151 40.443891 28 955508 401890 35.188063 40.44902 29 2442331 5137184 35.186128 40.448196 30 774225 41232 35.174386 40.436426 31 2323786 836001 35.161695 40.427101 32 1663952 5450025 35.163097 40.428304 33 859836 133148 35.160179 40.426471 34 2451250 2767462 35.147598 40.417462 35 2157761 3808141 35.162309 40.426655 36 107521141 2214887 35.186555 40.444768 37 0 4171700 35.179727 40.440031 38 0 386290 35.177917 40.439821 39 0 4925812 35.17219 40.436343 40 0 0 35.164267 40.428933 41 0 350116601 35.153623 40.420308 42 0 0 35.147734 40.416005 43 0 0 35.14926 40.416741 44 0 0 35.15117 40.417717 45 0 0 35.158076 40.422936 46 0 0 35.156565 40.421588 47 0 0 35.141591 40.412494 48 0 0 35.132413 40.405986 49 0 0 35.131098 40.404574 50 0 0 35.120499 40.396464 51 0 0 35.110558 40.388753 52 0 0 35.096783 40.379764 53 0 0 35.083062 40.373026 54 0 0 35.069351 40.362007 55 0 0 35.056139 40.351294 56 0 0 35.030525 40.336249 57 0 0 35.011777 40.321263 58 0 0 34.980772 40.297148 59 0 0 34.942644 40.269436 60 0 0 34.894275 40.233939 61 0 0 34.846429 40.198395 62 0 0 34.784552 40.152043 63 0 0 34.724474 40.105924 64 0 0 34.655497 40.0536 65 0 0 34.577933 39.994768 66 0 0 34.504781 39.939323 67 0 0 34.417055 39.874069 68 0 0 34.326536 39.806418 69 0 0 34.226308 39.729164 70 0 0 34.122925 39.649527 71 0 0 34.03381 39.574341 72 0 0 33.923135 39.488876 73 0 0 33.827105 39.411727 74 0 0 33.72932 39.33501 75 0 0 33.641275 39.26562 76 0 0 33.562566 39.203526 77 0 0 33.479546 39.140732 78 0 0 33.407679 39.086309 79 0 0 33.347059 39.032839 80 0 0 33.27694 38.977141 81 0 0 33.22738 38.938237 82 0 0 33.169252 38.885677 83 0 0 33.127271 38.854199 84 0 0 33.097283 38.829929 85 0 0 33.042071 38.782802 86 0 0 33.011517 38.754972 87 0 0 32.965246 38.716864 88 0 0 32.915236 38.672932 89 0 0 32.863531 38.631911 90 0 0 32.813215 38.590665 91 0 0 32.768469 38.550036 92 0 0 32.721595 38.508898 93 0 0 32.672767 38.468136 94 0 0 32.635177 38.437474 95 0 0 32.61671 38.422346 96 0 0 32.580461 38.390506 97 0 0 32.57574 38.386213 98 0 0 32.576322 38.386067 99 0 0 32.603596 38.404236 100 0 0 32.617172 38.413926 101 0 0 32.650359 38.441284 102 0 0 32.69505 38.475561 103 0 0 32.729744 38.500636 104 0 0 32.767585 38.526368 105 0 0 32.784812 38.538736 106 0 0 32.80035 38.548164 107 0 0 32.806154 38.549303 108 0 0 32.787758 38.532729 109 0 0 32.779612 38.528576 110 0 0 32.768129 38.519271 111 0 0 32.729204 38.487655 112 0 0 32.685511 38.452693 113 0 0 32.640007 38.412405 114 0 0 32.595561 38.377332 115 0 0 32.550529 38.339813 116 0 0 32.53594 38.330713 117 0 0 32.505528 38.307095 118 0 0 32.50811 38.308923 119 0 0 32.529258 38.331131 120 0 0 32.528939 38.328587 121 0 0 32.555961 38.348896 122 0 0 32.580583 38.366975 123 0 0 32.589538 38.371595 124 0 0 32.603929 38.382546 125 0 0 32.632232 38.400448 126 0 0 32.650605 38.410017 127 0 0 32.669033 38.421096 128 0 0 32.655992 38.406365 129 0 0 32.633584 38.389064 130 0 0 32.608184 38.367911 131 0 0 32.594851 38.356129 132 0 0 32.587134 38.348598 133 0 0 32.584206 38.340147 134 0 0 32.586775 38.343646 135 0 0 32.572984 38.334069 136 0 0 32.566217 38.326886 137 0 0 32.555873 38.317525 138 0 0 32.58066 38.336935 139 0 0 32.592088 38.345266 140 0 0 32.608836 38.361361 141 0 0 32.635031 38.384242 142 0 0 32.659603 38.405224 143 0 0 32.666979 38.411279 144 0 0 32.669859 38.405518 145 0 0 32.668641 38.403115 146 0 0 32.653651 38.3911 147 0 0 32.63355 38.364558 148 0 0 32.613256 38.350963 149 0 0 32.588925 38.326513 150 0 0 32.530138 38.275977 151 0 0 32.521663 38.275089 152 0 0 32.532677 38.286688 153 0 0 32.513382 38.2658 154 0 0 32.523893 38.27579 155 0 0 32.509576 38.261796 156 0 0 32.508235 38.267287 157 0 0 32.537009 38.286158 158 0 0 32.557846 38.300062 159 0 0 32.573274 38.315032 160 0 0 32.609173 38.345111 161 0 0 32.64075 38.368317 162 0 0 32.669355 38.385868 163 0 0 32.677985 38.390812 164 0 0 32.710252 38.418966 165 0 0 32.709444 38.421384 166 0 0 32.692669 38.401315 167 0 0 32.69037 38.396199 168 0 0 32.65412 38.360606 169 0 0 32.634803 38.340798 170 0 0 32.602073 38.311668 171 0 0 32.569739 38.286508 172 0 0 32.581474 38.297595 173 0 0 32.564613 38.286958 174 0 0 32.599513 38.316975 175 0 0 32.590744 38.312631 176 0 0 32.644819 38.352354 177 0 0 32.682776 38.387465 178 0 0 32.703914 38.403034 179 0 0 32.746526 38.43866 180 0 0 32.805627 38.490379 181 0 0 32.846015 38.515285 182 0 0 32.896443 38.56194 183 0 0 32.925402 38.593449 184 0 0 32.950278 38.616322 185 0 0 32.9905 38.647662 186 0 0 33.026694 38.674441 187 0 0 33.043537 38.687959 188 0 0 33.064142 38.7053 189 0 0 33.083053 38.724802 190 0 0 33.095463 38.732068 191 0 0 33.073359 38.726636 192 0 0 33.056538 38.709423 193 0 0 33.030873 38.693696 194 0 0 33.010761 38.693535 195 0 0 33.012895 38.699698 196 0 0 33.016089 38.703743 197 0 0 32.989403 38.685867 198 0 0 33.017391 38.725308 199 0 0 32.98975 38.709928 200 0 0 32.985912 38.704315 201 0 0 32.936945 38.683514 202 0 0 32.968311 38.70322 203 0 0 32.929082 38.68613 204 0 0 32.930311 38.694965 205 0 0 32.931814 38.693935 206 0 0 32.906193 38.686303 207 0 0 32.938542 38.710527 208 0 0 32.919982 38.699323 209 0 0 32.852992 38.657499 210 0 0 32.839353 38.653964 211 0 0 32.792102 38.625974 212 0 0 32.809947 38.64237 213 0 0 32.796228 38.62448 214 0 0 32.697462 38.573177 215 0 0 32.781093 38.627034 216 0 0 32.731577 38.590638 217 0 0 32.710918 38.580879 218 0 0 32.668321 38.551186 219 0 0 32.732939 38.614026 220 0 0 32.684574 38.563911 221 0 0 32.60032 38.529723 222 0 0 32.627638 38.539206 223 0 0 32.595338 38.52851 224 0 0 32.566206 38.502047 225 0 0 32.514258 38.466411 226 0 0 32.573542 38.499211 227 0 0 32.569238 38.498541 228 0 0 32.555773 38.497958 229 0 0 32.471081 38.432204 230 0 0 32.495891 38.439279 231 0 0 32.475043 38.445893 232 0 0 32.518073 38.483689 233 0 0 32.425937 38.393766 234 0 0 32.358551 38.376755 235 0 0 32.373538 38.391069 236 0 0 32.251642 38.286639 237 0 0 32.311459 38.354971 238 0 0 32.234595 38.289625 239 0 0 32.338218 38.376058 240 0 0 32.247707 38.305148 241 0 0 32.247922 38.303765 242 0 0 32.163927 38.274656 243 0 0 32.180838 38.236903 244 0 0 32.170419 38.255468 245 0 0 32.117154 38.224845 246 0 0 32.021696 38.157913 247 0 0 32.075325 38.204259 248 0 0 32.055624 38.1969 249 0 0 32.015755 38.13855 250 0 0 32.074592 38.21339 251 0 0 31.916727 38.099875 252 0 0 31.922074 38.103434 253 0 0 31.905854 38.069335 254 0 0 31.954852 38.142678 255 0 0 31.712858 37.970556 256 0 0 31.861343 38.083905 257 0 0 31.857306 38.081648 258 0 0 31.642682 37.913342 259 0 0 31.707716 37.965877 260 0 0 31.724341 37.990663 261 0 0 31.58297 37.891499 262 0 0 31.573357 37.869467 263 0 0 31.583686 37.893761 264 0 0 31.393943 37.793692 265 0 0 31.450919 37.792742 266 0 0 31.365249 37.743877 267 0 0 31.266561 37.693872 268 0 0 31.261821 37.672171 269 0 0 31.202767 37.66624 270 0 0 31.170578 37.62895 271 0 0 31.156288 37.630284 272 0 0 31.097892 37.609346 273 0 0 30.882345 37.452947 274 0 0 30.885698 37.460923 275 0 0 30.772269 37.35186 276 0 0 30.687949 37.326555 277 0 0 30.698871 37.267755 278 0 0 30.57721 37.223744 279 0 0 30.557552 37.228352 280 0 0 30.514146 37.220932 281 0 0 30.369467 37.077891 282 0 0 30.262068 37.002967 283 0 0 30.320808 37.034124 284 0 0 30.191142 36.940709 285 0 0 30.181868 36.948775 286 0 0 30.149129 37.007949 287 0 0 30.049612 36.823256 288 0 0 30.011572 36.846768 289 0 0 29.9395 36.765723 290 0 0 29.886124 36.763321 291 0 0 29.883721 36.761356 292 0 0 29.774049 36.686577 293 0 0 29.654095 36.584066 294 0 0 29.274946 36.332775 295 0 0 29.350756 36.354141 296 0 0 29.240206 36.293729 297 0 0 29.566711 36.552508 298 0 0 29.432642 36.463347 299 0 0 29.001734 36.134065 300 0 0 29.03495 36.120117 301 0 0 28.987599 36.126126 302 0 0 29.329 36.332667 303 0 0 28.81353 35.911789 304 0 0 28.848083 36.005039 305 0 0 28.635626 35.929289 306 0 0 28.732649 35.98987 307 0 0 28.665935 35.877524 308 0 0 28.490407 35.820621 309 0 0 28.838213 35.954508 310 0 0 28.61061 35.890893 311 0 0 28.475921 35.77847 312 0 0 28.697376 35.891601 313 0 0 28.277851 35.524465 314 0 0 28.420072 35.743369 315 0 0 28.523589 35.811292 316 0 0 28.004184 35.508787 317 0 0 28.398922 35.657981 318 0 0 28.526523 35.854289 319 0 0 28.329386 35.720488 320 0 0 27.260258 34.9195 321 0 0 27.90653 35.293214 322 0 0 28.776034 35.926296 323 0 0 28.52093 35.851163 324 0 0 28.273519 35.475029 325 0 0 29.232692 36.241026 326 0 0 27.419355 35.031541 327 0 0 27.995238 35.347619 328 0 0 28.649596 35.716083 329 0 0 28.418182 35.760606 330 0 0 28.498316 35.698092 331 0 0 28.04943 35.6109 332 0 0 27.742358 35.462882 333 0 0 27.551546 34.90378 334 0 0 28.375723 35.776493 335 0 0 28.805369 35.973154 336 0 0 28.323077 35.871795 337 0 0 28.234783 35.402899 338 0 0 28.798077 35.932692 339 0 0 28.311111 35.496296 340 0 0 30.025641 36.769231 341 0 0 29.567164 36.472637 342 0 0 29.892857 37.244048 343 0 0 28.294118 35.006536 344 0 0 30.130435 36.956522 345 0 0 29.833333 36.547619 346 0 0 26.717949 33.871795 347 0 0 26.529412 34.098039 348 0 0 31.310345 37.448276 349 0 0 29.5 36.423077 350 0 0 27.68 35.16 351 0 0 29.136364 36.545455 352 0 0 26.529412 34.72549 353 0 0 28.384615 36.512821 354 0 0 24.6 33.433333 355 0 0 26.1 33.933333 356 0 0 29.25 36.875 357 0 0 27 36.047619 358 0 0 24.571429 30.857143 359 0 0 32.166667 37.833333 360 0 0 20 27.933333 361 0 0 34 39.666667 362 0 0 24 33.333333 363 0 0 24 29.555556 364 0 0 22.666667 32.555556 365 0 0 25.5 33.5 366 0 0 34 39 367 0 0 14 20 368 0 0 36 41 369 0 0 20 34 370 0 0 26 33.666667 371 0 0 36 41 372 0 0 24 35.333333 373 0 0 16 27.333333 374 0 0 26 36 375 0 0 10 17.333333 376 0 0 26 36 377 0 0 32 38.666667 378 0 0 34 39.333333