## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5419-Z0116-CAGTTATGTGCTGAT/441525-L5419-Z0116-CAGTTATGTGCTGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5419-Z0116-CAGTTATGTGCTGAT/441525-L5419-Z0116-CAGTTATGTGCTGAT_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 02:59:53 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 999810 999810 115 115097867 115097867 110328445 110328445 101469011 101469011 0 0 0.958562 0.881589 0 0.958562 0.881589 0 345293601 345293601 338889836 338889836 324857972 324857972 301872985 301872985 0.981454 0.940817 0.87425 0.981454 0.940817 0.87425 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 813 2 35.993544 40.995155 1 9460 0 35.982621 40.988379 2 11723 3455 35.992314 40.993763 3 29965 1008 35.978333 40.982564 4 49657 40547 35.989688 40.991917 5 98181 17036 35.994171 40.995291 6 108000 107736 35.977668 40.981226 7 175994 145776 35.980463 40.986682 8 199551 136478 35.9894 40.991646 9 228019 101289 35.967085 40.972305 10 247300 482597 35.856199 40.915648 11 293200 54960 35.911703 40.933402 12 352137 690202 34.99521 40.157296 13 353628 210687 33.078294 39.196594 14 458544 1000093 35.867597 40.91876 15 360744 365555 35.841553 40.886524 16 394676 483144 35.789147 40.812175 17 505782 1131712 35.894632 40.909689 18 541541 713045 35.767105 40.806518 19 350507 718443 35.743043 40.809591 20 479077 1007795 35.891292 40.928642 21 637725 1292697 35.825556 40.876278 22 295645 556913 35.552084 40.702916 23 978756 1129405 35.249603 40.500105 24 538172 1073841 35.253324 40.499394 25 525047 439042 35.268135 40.510205 26 1717074 2437817 35.199967 40.459576 27 329463 776572 35.228909 40.477079 28 930845 338636 35.256493 40.496067 29 2427630 4979146 35.261941 40.499784 30 691716 38954 35.252006 40.49105 31 2216725 687290 35.254229 40.491349 32 1439295 5376956 35.25708 40.491519 33 771187 115767 35.246077 40.485327 34 2277602 2302421 35.242242 40.482153 35 2007914 3719017 35.250362 40.486743 36 92064572 1864983 35.28035 40.5082 37 0 4022531 35.284312 40.511911 38 0 301732 35.27011 40.502937 39 0 4555336 35.267079 40.498916 40 0 4 35.272189 40.503437 41 0 301872981 35.262543 40.49554 42 0 0 35.250019 40.486083 43 0 0 35.256196 40.490832 44 0 0 35.265292 40.496882 45 0 0 35.266464 40.496653 46 0 0 35.250932 40.486853 47 0 0 35.244681 40.481687 48 0 0 35.230318 40.471374 49 0 0 35.223742 40.466622 50 0 0 35.200531 40.45012 51 0 0 35.188957 40.443017 52 0 0 35.172028 40.43154 53 0 0 35.155028 40.419488 54 0 0 35.138099 40.406132 55 0 0 35.095426 40.373894 56 0 0 35.053117 40.343117 57 0 0 35.006332 40.311134 58 0 0 34.952162 40.269831 59 0 0 34.878505 40.216219 60 0 0 34.791452 40.153748 61 0 0 34.697565 40.082705 62 0 0 34.585153 39.995867 63 0 0 34.484155 39.918285 64 0 0 34.364034 39.826757 65 0 0 34.228897 39.728568 66 0 0 34.089667 39.625213 67 0 0 33.946031 39.517707 68 0 0 33.78584 39.396409 69 0 0 33.618215 39.265484 70 0 0 33.440011 39.125631 71 0 0 33.276303 38.994695 72 0 0 33.112087 38.86112 73 0 0 32.953201 38.732739 74 0 0 32.79513 38.607654 75 0 0 32.660508 38.500248 76 0 0 32.534705 38.401623 77 0 0 32.422082 38.315836 78 0 0 32.328628 38.245455 79 0 0 32.245097 38.176535 80 0 0 32.178557 38.122037 81 0 0 32.125933 38.075275 82 0 0 32.086439 38.03787 83 0 0 32.049503 38.007591 84 0 0 32.021872 37.97761 85 0 0 32.023237 37.977839 86 0 0 31.989796 37.943684 87 0 0 31.96395 37.92551 88 0 0 31.933425 37.891635 89 0 0 31.899931 37.86272 90 0 0 31.865246 37.830997 91 0 0 31.837453 37.803087 92 0 0 31.825951 37.788018 93 0 0 31.810464 37.770916 94 0 0 31.770713 37.734375 95 0 0 31.766502 37.735242 96 0 0 31.759984 37.732593 97 0 0 31.765203 37.733708 98 0 0 31.787984 37.748716 99 0 0 31.83965 37.792207 100 0 0 31.88154 37.822653 101 0 0 31.936494 37.866116 102 0 0 31.989494 37.90475 103 0 0 32.034615 37.938452 104 0 0 32.074487 37.967244 105 0 0 32.077871 37.967531 106 0 0 32.098458 37.977649 107 0 0 32.070793 37.952909 108 0 0 32.032738 37.92336 109 0 0 32.004881 37.903331 110 0 0 31.961448 37.870167 111 0 0 31.916362 37.829085 112 0 0 31.878669 37.799925 113 0 0 31.819219 37.750739 114 0 0 31.747133 37.697289 115 0 0 31.721041 37.680136 116 0 0 31.671138 37.639213 117 0 0 31.683619 37.653848 118 0 0 31.692498 37.659348 119 0 0 31.689086 37.651543 120 0 0 31.696249 37.662203 121 0 0 31.721391 37.678151 122 0 0 31.752618 37.70237 123 0 0 31.769797 37.707756 124 0 0 31.81778 37.741662 125 0 0 31.813373 37.734749 126 0 0 31.823013 37.743617 127 0 0 31.808805 37.727438 128 0 0 31.803578 37.713035 129 0 0 31.762418 37.677925 130 0 0 31.725411 37.645897 131 0 0 31.702728 37.631058 132 0 0 31.728994 37.642683 133 0 0 31.712722 37.638514 134 0 0 31.710949 37.634143 135 0 0 31.728121 37.650552 136 0 0 31.748306 37.665807 137 0 0 31.770189 37.682854 138 0 0 31.789174 37.696455 139 0 0 31.800754 37.702872 140 0 0 31.846246 37.740382 141 0 0 31.882716 37.768948 142 0 0 31.909907 37.786814 143 0 0 31.941283 37.815308 144 0 0 31.951547 37.825654 145 0 0 31.917871 37.788661 146 0 0 31.901222 37.776468 147 0 0 31.889482 37.769118 148 0 0 31.859352 37.732108 149 0 0 31.864989 37.739942 150 0 0 31.819135 37.698952 151 0 0 31.793909 37.686837 152 0 0 31.774233 37.670981 153 0 0 31.828724 37.715327 154 0 0 31.825474 37.707374 155 0 0 31.841817 37.722859 156 0 0 31.894415 37.768477 157 0 0 31.940567 37.811771 158 0 0 31.982831 37.837767 159 0 0 32.093791 37.930442 160 0 0 32.15359 37.972303 161 0 0 32.150013 37.968911 162 0 0 32.169624 37.989959 163 0 0 32.267559 38.061647 164 0 0 32.312874 38.102001 165 0 0 32.364206 38.136737 166 0 0 32.426223 38.188696 167 0 0 32.433156 38.198495 168 0 0 32.4437 38.197984 169 0 0 32.431739 38.192363 170 0 0 32.446564 38.196824 171 0 0 32.431023 38.17962 172 0 0 32.454857 38.216197 173 0 0 32.474869 38.239324 174 0 0 32.489191 38.240392 175 0 0 32.459042 38.228336 176 0 0 32.563744 38.317483 177 0 0 32.586967 38.333341 178 0 0 32.644179 38.384575 179 0 0 32.693262 38.424979 180 0 0 32.802417 38.514045 181 0 0 32.80515 38.516605 182 0 0 32.805075 38.529125 183 0 0 32.910718 38.606128 184 0 0 32.954032 38.645791 185 0 0 32.997688 38.681346 186 0 0 32.980584 38.677854 187 0 0 33.009287 38.686141 188 0 0 33.010072 38.699211 189 0 0 33.099082 38.787606 190 0 0 33.086587 38.751627 191 0 0 33.097338 38.778213 192 0 0 33.095952 38.777873 193 0 0 33.101582 38.779027 194 0 0 33.101095 38.782189 195 0 0 33.089863 38.777338 196 0 0 33.066296 38.764428 197 0 0 33.04329 38.770715 198 0 0 33.105343 38.817568 199 0 0 33.084535 38.813795 200 0 0 33.09649 38.828457 201 0 0 33.127271 38.866502 202 0 0 33.124847 38.870373 203 0 0 33.164686 38.895856 204 0 0 33.161312 38.895737 205 0 0 33.132922 38.871193 206 0 0 33.103193 38.869256 207 0 0 33.111612 38.87646 208 0 0 33.11811 38.878491 209 0 0 33.089167 38.868978 210 0 0 33.069223 38.858975 211 0 0 33.092834 38.881327 212 0 0 33.044645 38.841139 213 0 0 33.049238 38.843329 214 0 0 33.022467 38.832275 215 0 0 32.982049 38.790251 216 0 0 32.939568 38.783945 217 0 0 32.96557 38.804416 218 0 0 32.995903 38.834234 219 0 0 33.061766 38.869416 220 0 0 32.968188 38.809467 221 0 0 32.999715 38.823444 222 0 0 32.946625 38.8065 223 0 0 32.854371 38.746583 224 0 0 32.780553 38.719019 225 0 0 32.877284 38.749569 226 0 0 32.879506 38.736495 227 0 0 32.880807 38.759397 228 0 0 32.907868 38.771152 229 0 0 32.889071 38.779312 230 0 0 32.788913 38.704063 231 0 0 32.855478 38.773934 232 0 0 32.857736 38.767212 233 0 0 32.886288 38.764343 234 0 0 32.703141 38.661783 235 0 0 32.781005 38.684545 236 0 0 32.767538 38.708316 237 0 0 32.857892 38.765471 238 0 0 32.817128 38.740521 239 0 0 32.770222 38.727506 240 0 0 32.646131 38.611887 241 0 0 32.766662 38.719499 242 0 0 32.715457 38.638013 243 0 0 32.62351 38.612936 244 0 0 32.628167 38.636284 245 0 0 32.592674 38.611046 246 0 0 32.685141 38.654713 247 0 0 32.582197 38.566748 248 0 0 32.610992 38.617297 249 0 0 32.590131 38.595412 250 0 0 32.371524 38.47695 251 0 0 32.516975 38.566579 252 0 0 32.422708 38.506904 253 0 0 32.451638 38.510725 254 0 0 32.418628 38.521192 255 0 0 32.295656 38.416935 256 0 0 32.366053 38.458759 257 0 0 32.267415 38.378804 258 0 0 32.105519 38.302319 259 0 0 32.020219 38.216176 260 0 0 32.248578 38.425966 261 0 0 32.16871 38.359186 262 0 0 32.228526 38.412146 263 0 0 32.075511 38.291255 264 0 0 32.044543 38.248912 265 0 0 32.085302 38.328292 266 0 0 32.077127 38.262473 267 0 0 31.798291 38.142776 268 0 0 31.886211 38.130021 269 0 0 31.852459 38.121143 270 0 0 31.726105 38.097379 271 0 0 31.648515 37.9967 272 0 0 31.574485 37.931414 273 0 0 31.67838 38.048909 274 0 0 31.486354 37.858624 275 0 0 31.613208 37.961802 276 0 0 31.5318 37.911035 277 0 0 31.534716 37.925094 278 0 0 31.573703 37.948211 279 0 0 31.251348 37.809167 280 0 0 31.416948 37.776891 281 0 0 31.380982 37.827246 282 0 0 31.261866 37.742762 283 0 0 31.437542 37.83134 284 0 0 31.378518 37.864219 285 0 0 31.244058 37.791179 286 0 0 31.353005 37.783728 287 0 0 31.38204 37.83346 288 0 0 31.657884 38.006947 289 0 0 31.54401 37.985058 290 0 0 31.573062 37.931667 291 0 0 31.419748 37.863564 292 0 0 31.452999 37.812593 293 0 0 31.777471 38.063602 294 0 0 31.561114 37.893975 295 0 0 31.583981 37.979612 296 0 0 31.548048 37.985819 297 0 0 31.756812 38.111225 298 0 0 31.633914 38.031872 299 0 0 31.44281 37.861837 300 0 0 31.747632 38.051439 301 0 0 31.582854 37.914269 302 0 0 31.509221 37.963315 303 0 0 31.714548 38.035045 304 0 0 31.696338 38.052609 305 0 0 31.563851 37.919886 306 0 0 31.623403 37.979153 307 0 0 31.607939 38.045032 308 0 0 31.840746 38.167623 309 0 0 31.765533 38.049556 310 0 0 31.436968 37.814901 311 0 0 32.00641 38.238782 312 0 0 32.208782 38.395195 313 0 0 31.329614 37.757654 314 0 0 31.773736 38.060929 315 0 0 31.483395 37.815498 316 0 0 31.99709 38.261235 317 0 0 31.709054 37.962699 318 0 0 31.606349 37.952381 319 0 0 31.466965 37.867488 320 0 0 31.456392 37.938272 321 0 0 31.265152 37.757155 322 0 0 31.256684 37.663993 323 0 0 31.314972 37.588983 324 0 0 30.948485 37.60303 325 0 0 31.267101 37.747014 326 0 0 31.367418 37.748122 327 0 0 31.541899 37.94103 328 0 0 31.357143 37.89418 329 0 0 31.215686 37.689906 330 0 0 31.254042 37.759045 331 0 0 31.537313 37.902985 332 0 0 30.815013 37.238606 333 0 0 31.011594 37.57971 334 0 0 31.540453 37.81877 335 0 0 31.254355 37.832753 336 0 0 30.690299 37.20398 337 0 0 31.199187 37.688347 338 0 0 31.361233 37.668135 339 0 0 31.386935 37.80402 340 0 0 31.048649 37.623423 341 0 0 32.195266 38.128205 342 0 0 32.484277 38.668763 343 0 0 32.310345 38.450575 344 0 0 31.820312 38.294271 345 0 0 32.078261 38.049275 346 0 0 30.57 37.543333 347 0 0 30.141304 36.902174 348 0 0 31.329268 37.894309 349 0 0 31.181818 37.246753 350 0 0 29.140845 36.488263 351 0 0 29.111111 35.873016 352 0 0 28.280702 35.385965 353 0 0 29.06383 36.687943 354 0 0 29.425 36.725 355 0 0 31.121212 37.707071 356 0 0 29.178571 36.214286 357 0 0 30.52 36.733333 358 0 0 30.76 37.586667 359 0 0 31.26087 37.144928 360 0 0 29.3 35.883333 361 0 0 28.75 36.020833 362 0 0 29.8 37.177778 363 0 0 26.769231 33.615385 364 0 0 30.416667 36.833333 365 0 0 31.75 38.791667 366 0 0 29.714286 37.238095 367 0 0 29.166667 35.777778 368 0 0 34.4 39.866667 369 0 0 35 40.416667 370 0 0 36 41 371 0 0 36 41 372 0 0 34.666667 40.222222 373 0 0 34.666667 40.222222 374 0 0 28 36 375 0 0 35.333333 40.111111 376 0 0 36 41 377 0 0 36 41 378 0 0 36 41 379 0 0 36 41 380 0 0 36 41 381 0 0 36 41 382 0 0 29 37 383 0 0 29 37 384 0 0 36 41 385 0 0 36 41 386 0 0 36 41 387 0 0 34 39 388 0 0 16 24.666667 389 0 0 7 20.333333 390 0 0 29 37 391 0 0 10 22.333333 392 0 0 29 35 393 0 0 5 19.666667 394 0 0 5 24.333333