## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5377-Z0056-CTTATGCTATCAGAT/441525-L5377-Z0056-CTTATGCTATCAGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5377-Z0056-CTTATGCTATCAGAT/441525-L5377-Z0056-CTTATGCTATCAGAT_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 02:54:26 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 1000160 1000160 126 126915928 126915928 122188194 122188194 113237744 113237744 0 0 0.962749 0.892226 0 0.962749 0.892226 0 380747784 380747784 374452379 374452379 360202263 360202263 336228493 336228493 0.983466 0.946039 0.883074 0.983466 0.946039 0.883074 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 791 0 35.986936 40.989989 1 9692 0 35.982389 40.987253 2 11939 3885 35.99545 40.996266 3 30360 1041 35.987624 40.989987 4 50087 41868 35.99248 40.993833 5 98113 15886 35.996144 40.996725 6 106371 108487 35.982334 40.98629 7 176181 141510 35.984627 40.989163 8 193040 136219 35.990484 40.992082 9 227808 98085 35.964571 40.97008 10 240398 480250 35.878948 40.929788 11 286006 53639 35.912635 40.934598 12 343272 681690 35.25485 40.373078 13 348271 202506 33.792169 39.63236 14 446025 980453 35.885244 40.930199 15 359489 360663 35.842594 40.888616 16 387630 455444 35.796808 40.819218 17 506849 1120762 35.890186 40.905255 18 541698 699327 35.752766 40.797668 19 363714 713690 35.743132 40.807432 20 484404 1014145 35.897789 40.930745 21 637171 1316386 35.814622 40.860983 22 306016 563354 35.583037 40.712301 23 987522 1137612 35.219874 40.437299 24 555104 1128994 35.298887 40.515033 25 529528 462807 35.336611 40.54605 26 1727245 2437402 35.254132 40.473815 27 346540 834747 35.289284 40.515995 28 949606 350481 35.28252 40.512196 29 2427314 5004188 35.272769 40.502582 30 733389 36654 35.320732 40.534795 31 2271034 741871 35.312039 40.528069 32 1491654 5431982 35.288074 40.502727 33 809188 113263 35.313747 40.526016 34 2381676 2388442 35.312953 40.529382 35 2162812 3856573 35.330687 40.542895 36 103387991 1909962 35.349303 40.55666 37 0 4266677 35.349628 40.557346 38 0 329632 35.343205 40.553316 39 0 4898714 35.339954 40.55053 40 0 0 35.332349 40.543568 41 0 336228493 35.326481 40.538357 42 0 0 35.326523 40.537729 43 0 0 35.321234 40.535546 44 0 0 35.336903 40.545109 45 0 0 35.331581 40.54292 46 0 0 35.322677 40.534744 47 0 0 35.314863 40.528342 48 0 0 35.28905 40.509764 49 0 0 35.289244 40.510888 50 0 0 35.294648 40.515414 51 0 0 35.287714 40.512361 52 0 0 35.242694 40.480567 53 0 0 35.196448 40.460489 54 0 0 35.210845 40.464281 55 0 0 35.200813 40.457952 56 0 0 35.128988 40.421539 57 0 0 35.168849 40.432186 58 0 0 35.14519 40.410553 59 0 0 35.09876 40.37507 60 0 0 35.047373 40.33591 61 0 0 34.97834 40.284073 62 0 0 34.905979 40.228191 63 0 0 34.831127 40.168824 64 0 0 34.735737 40.096331 65 0 0 34.63442 40.022766 66 0 0 34.523594 39.938902 67 0 0 34.414509 39.857674 68 0 0 34.288882 39.763597 69 0 0 34.158824 39.662267 70 0 0 34.024326 39.555973 71 0 0 33.894511 39.451548 72 0 0 33.770498 39.350697 73 0 0 33.63489 39.242713 74 0 0 33.526494 39.157961 75 0 0 33.413889 39.07118 76 0 0 33.299485 38.982546 77 0 0 33.219564 38.924067 78 0 0 33.149015 38.867913 79 0 0 33.071282 38.808407 80 0 0 33.025431 38.764684 81 0 0 32.983503 38.729267 82 0 0 32.942765 38.691922 83 0 0 32.919391 38.670012 84 0 0 32.903977 38.655415 85 0 0 32.866344 38.626205 86 0 0 32.852696 38.61096 87 0 0 32.812076 38.578743 88 0 0 32.778691 38.549427 89 0 0 32.739856 38.514735 90 0 0 32.704491 38.483666 91 0 0 32.663226 38.444493 92 0 0 32.62306 38.409208 93 0 0 32.587945 38.37918 94 0 0 32.540147 38.34019 95 0 0 32.503155 38.309848 96 0 0 32.47477 38.287685 97 0 0 32.461382 38.276682 98 0 0 32.45349 38.268732 99 0 0 32.485491 38.296149 100 0 0 32.509777 38.312602 101 0 0 32.559032 38.351684 102 0 0 32.606375 38.388115 103 0 0 32.637907 38.40875 104 0 0 32.68642 38.443446 105 0 0 32.709209 38.46065 106 0 0 32.736001 38.478206 107 0 0 32.744706 38.481481 108 0 0 32.772203 38.506291 109 0 0 32.783949 38.511839 110 0 0 32.765585 38.498042 111 0 0 32.748297 38.482874 112 0 0 32.707579 38.449925 113 0 0 32.663176 38.413296 114 0 0 32.60377 38.363793 115 0 0 32.579259 38.342476 116 0 0 32.524855 38.303376 117 0 0 32.520718 38.302808 118 0 0 32.507195 38.294251 119 0 0 32.520866 38.307199 120 0 0 32.513253 38.301019 121 0 0 32.514874 38.303905 122 0 0 32.523145 38.305808 123 0 0 32.547453 38.321519 124 0 0 32.545519 38.31495 125 0 0 32.565133 38.333283 126 0 0 32.571607 38.334656 127 0 0 32.571401 38.3311 128 0 0 32.566154 38.322769 129 0 0 32.585374 38.336281 130 0 0 32.556957 38.311622 131 0 0 32.531921 38.286748 132 0 0 32.505778 38.266753 133 0 0 32.515535 38.274491 134 0 0 32.501773 38.261633 135 0 0 32.494332 38.252618 136 0 0 32.487737 38.250151 137 0 0 32.481088 38.241646 138 0 0 32.481022 38.244303 139 0 0 32.481822 38.24634 140 0 0 32.483042 38.250835 141 0 0 32.539752 38.289561 142 0 0 32.547623 38.296215 143 0 0 32.547819 38.29228 144 0 0 32.540249 38.290376 145 0 0 32.538964 38.279105 146 0 0 32.509105 38.256088 147 0 0 32.482146 38.235844 148 0 0 32.462494 38.219677 149 0 0 32.414131 38.179027 150 0 0 32.391546 38.160693 151 0 0 32.375046 38.147693 152 0 0 32.358437 38.133291 153 0 0 32.348368 38.123723 154 0 0 32.369683 38.140024 155 0 0 32.343958 38.11644 156 0 0 32.340782 38.115688 157 0 0 32.355536 38.128366 158 0 0 32.369469 38.135465 159 0 0 32.427241 38.187844 160 0 0 32.440032 38.189858 161 0 0 32.496821 38.239917 162 0 0 32.487632 38.230608 163 0 0 32.519087 38.256367 164 0 0 32.511598 38.25508 165 0 0 32.505641 38.24111 166 0 0 32.521771 38.253769 167 0 0 32.500462 38.232641 168 0 0 32.498281 38.220144 169 0 0 32.422461 38.164356 170 0 0 32.375523 38.129017 171 0 0 32.356443 38.112658 172 0 0 32.356474 38.104021 173 0 0 32.380213 38.130143 174 0 0 32.350406 38.103513 175 0 0 32.387513 38.1428 176 0 0 32.431875 38.18077 177 0 0 32.485052 38.223483 178 0 0 32.535828 38.263507 179 0 0 32.58168 38.297985 180 0 0 32.650356 38.357306 181 0 0 32.702189 38.399117 182 0 0 32.751053 38.439739 183 0 0 32.77154 38.455005 184 0 0 32.809325 38.492874 185 0 0 32.837247 38.516623 186 0 0 32.859866 38.529477 187 0 0 32.887959 38.559724 188 0 0 32.916624 38.581569 189 0 0 32.924253 38.592225 190 0 0 32.910646 38.576277 191 0 0 32.917683 38.592364 192 0 0 32.913888 38.599946 193 0 0 32.877031 38.567881 194 0 0 32.87885 38.573122 195 0 0 32.842975 38.562363 196 0 0 32.792845 38.525034 197 0 0 32.775866 38.521814 198 0 0 32.813574 38.555672 199 0 0 32.793758 38.534515 200 0 0 32.832355 38.575044 201 0 0 32.822378 38.573487 202 0 0 32.799647 38.561046 203 0 0 32.746373 38.541886 204 0 0 32.776733 38.565121 205 0 0 32.755689 38.553433 206 0 0 32.70538 38.517913 207 0 0 32.707528 38.52116 208 0 0 32.745397 38.550113 209 0 0 32.661661 38.508749 210 0 0 32.612682 38.465133 211 0 0 32.635845 38.498599 212 0 0 32.566552 38.436695 213 0 0 32.533112 38.421118 214 0 0 32.546918 38.442735 215 0 0 32.524806 38.436284 216 0 0 32.498403 38.393343 217 0 0 32.481764 38.404326 218 0 0 32.486691 38.399743 219 0 0 32.435084 38.376939 220 0 0 32.399677 38.351481 221 0 0 32.431462 38.381445 222 0 0 32.327024 38.292306 223 0 0 32.366269 38.34529 224 0 0 32.262119 38.262995 225 0 0 32.295214 38.27649 226 0 0 32.211943 38.226707 227 0 0 32.319715 38.284942 228 0 0 32.212503 38.219192 229 0 0 32.176376 38.210391 230 0 0 32.131603 38.175752 231 0 0 32.129669 38.158943 232 0 0 32.122986 38.200735 233 0 0 32.13559 38.207873 234 0 0 32.103108 38.193126 235 0 0 32.054856 38.127587 236 0 0 32.040905 38.130994 237 0 0 32.022203 38.132799 238 0 0 31.993914 38.09248 239 0 0 31.91265 38.052346 240 0 0 32.046576 38.158922 241 0 0 31.981772 38.114285 242 0 0 31.888525 38.047318 243 0 0 31.924643 38.067771 244 0 0 31.956631 38.102689 245 0 0 31.852182 38.017568 246 0 0 31.678397 37.914009 247 0 0 31.844282 38.026724 248 0 0 31.767713 37.972913 249 0 0 31.507622 37.799978 250 0 0 31.672516 37.929025 251 0 0 31.557504 37.834385 252 0 0 31.63354 37.885032 253 0 0 31.446323 37.741909 254 0 0 31.447092 37.767123 255 0 0 31.512306 37.796691 256 0 0 31.394924 37.796157 257 0 0 31.394055 37.806214 258 0 0 31.31364 37.722594 259 0 0 31.323305 37.675661 260 0 0 31.150173 37.630958 261 0 0 31.320463 37.740112 262 0 0 31.077291 37.532625 263 0 0 31.046289 37.536291 264 0 0 31.14318 37.635602 265 0 0 31.001168 37.431464 266 0 0 30.942539 37.401524 267 0 0 30.946367 37.533105 268 0 0 30.816602 37.416452 269 0 0 30.819145 37.362813 270 0 0 30.795152 37.411289 271 0 0 30.416285 37.122195 272 0 0 30.679492 37.285178 273 0 0 30.621601 37.208939 274 0 0 30.557302 37.212597 275 0 0 30.224369 36.970689 276 0 0 30.579204 37.253452 277 0 0 30.069992 36.89131 278 0 0 30.282338 37.034522 279 0 0 30.229342 37.015908 280 0 0 29.790909 36.760606 281 0 0 29.986811 36.737635 282 0 0 29.633803 36.52566 283 0 0 30.008105 36.848193 284 0 0 29.830149 36.780786 285 0 0 30.011583 36.785071 286 0 0 29.614458 36.628992 287 0 0 29.376338 36.420729 288 0 0 29.302786 36.344066 289 0 0 29.462821 36.448718 290 0 0 29.270432 36.27021 291 0 0 29.149337 36.290533 292 0 0 29.068764 36.185564 293 0 0 28.971669 36.081674 294 0 0 29.324717 36.466074 295 0 0 28.818803 36.008832 296 0 0 29.007156 36.23554 297 0 0 28.599057 35.883333 298 0 0 28.975 36.105667 299 0 0 28.162766 35.571277 300 0 0 29.095768 36.21418 301 0 0 28.81338 36.054773 302 0 0 28.780822 36.052719 303 0 0 28.860558 36.051793 304 0 0 28.096317 35.568933 305 0 0 28.455371 35.792738 306 0 0 28.203883 35.710356 307 0 0 29.240484 36.312572 308 0 0 28.598113 35.851572 309 0 0 28.739837 35.863144 310 0 0 28.511879 35.942405 311 0 0 28.624424 35.966974 312 0 0 28.299505 35.660891 313 0 0 27.789894 35.161348 314 0 0 27.945559 35.326648 315 0 0 28.544304 35.894515 316 0 0 29.78853 36.709677 317 0 0 29.222222 36.051086 318 0 0 28.526087 36.075362 319 0 0 27.914286 35.45873 320 0 0 28.25 35.704861 321 0 0 27.55618 35.116105 322 0 0 27.715232 35.07947 323 0 0 27.536232 34.910628 324 0 0 28.296 35.610667 325 0 0 28.034783 35.333333 326 0 0 27.737374 35.686869 327 0 0 26.102273 34.833333 328 0 0 27.126582 34.485232 329 0 0 27.736111 35.777778 330 0 0 25.761905 33.798942 331 0 0 28.857143 35.97619 332 0 0 26.533333 33.948148 333 0 0 26.74359 34.957265 334 0 0 25.828571 33.438095 335 0 0 29.393939 36.212121 336 0 0 22.571429 31.809524 337 0 0 26.8 34.68 338 0 0 30.368421 37.684211 339 0 0 29.705882 36.705882 340 0 0 28.090909 36.424242 341 0 0 25.1 32.6 342 0 0 31.285714 37.761905 343 0 0 27.5 35.222222 344 0 0 24.8 31.6 345 0 0 25.2 32.133333 346 0 0 28.333333 36.777778 347 0 0 25 31.333333 348 0 0 31 38.777778 349 0 0 30 35.222222 350 0 0 26.5 34 351 0 0 36 41 352 0 0 36 41 353 0 0 36 41 354 0 0 36 41 355 0 0 36 41 356 0 0 36 41 357 0 0 36 41 358 0 0 36 41 359 0 0 36 41 360 0 0 36 41