## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/data/Runs/415630/output/415630-20250125_0254/415630-L3451-Z0011-CACGCACTGCCAGAT/415630-L3451-Z0011-CACGCACTGCCAGAT_sample.recal.bam OUTPUT=/data/Runs/415630/output/415630-20250125_0254/415630-L3451-Z0011-CACGCACTGCCAGAT/415630-L3451-Z0011-CACGCACTGCCAGAT_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: Sun Jan 26 12:31:02 EST 2025 ## 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 704153 704153 228 160910723 160910723 156386442 156386442 145947531 145947531 0 0 0.971883 0.907009 0 0.971883 0.907009 0 482732169 482732169 477349904 477349904 461738180 461738180 436739067 436739067 0.98885 0.95651 0.904723 0.98885 0.95651 0.904723 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 1368 2 35.139279 40.325068 1 19953 6 32.349451 38.596448 2 25402 14465 33.37634 39.175068 3 51967 3545 33.623994 39.325389 4 68288 82882 33.689266 39.369652 5 170478 15214 33.704762 39.382666 6 61461 213481 33.742451 39.412858 7 245305 238869 33.732412 39.402313 8 106161 142125 33.762747 39.421688 9 206939 139386 33.776527 39.436287 10 240051 400326 33.802682 39.453319 11 268260 98688 33.828002 39.465902 12 307410 519657 33.821395 39.466466 13 216944 199353 33.850908 39.485215 14 492324 694875 33.885738 39.51117 15 384924 464697 33.909721 39.529134 16 267098 168412 33.912214 39.532746 17 516147 740219 33.933345 39.544843 18 542127 892939 33.950609 39.557412 19 331674 353124 33.966919 39.568783 20 783045 749271 33.983737 39.580446 21 734148 1450143 34.014227 39.60082 22 445436 333007 34.033469 39.615089 23 1686166 2142868 34.042607 39.621129 24 687465 1143917 34.077343 39.648224 25 609330 512618 34.072695 39.64144 26 1936812 3161685 34.082485 39.648721 27 479066 1072233 34.101458 39.661461 28 775031 722205 34.11258 39.672353 29 2302412 4323777 34.12904 39.681905 30 773042 107933 34.136615 39.688976 31 2247465 1559580 34.142114 39.693779 32 3066943 3348677 34.160571 39.702768 33 802018 406148 34.17507 39.715028 34 2707629 5425314 34.194185 39.730029 35 2264230 2100126 34.208593 39.741176 36 134086204 4285659 34.219339 39.746761 37 0 2505897 34.214693 39.745133 38 0 771642 34.239178 39.760512 39 0 4488137 34.247878 39.766344 40 0 15 34.256665 39.77442 41 0 436739052 34.27163 39.783857 42 0 0 34.275569 39.786292 43 0 0 34.292066 39.796611 44 0 0 34.298129 39.799487 45 0 0 34.319731 39.817763 46 0 0 34.331505 39.824571 47 0 0 34.335137 39.826592 48 0 0 34.345272 39.83552 49 0 0 34.357828 39.842554 50 0 0 34.344942 39.833154 51 0 0 34.368443 39.851109 52 0 0 34.376406 39.855017 53 0 0 34.384027 39.8623 54 0 0 34.403494 39.875657 55 0 0 34.403407 39.874329 56 0 0 34.418444 39.885706 57 0 0 34.418384 39.886878 58 0 0 34.420205 39.886257 59 0 0 34.436946 39.899071 60 0 0 34.436778 39.897951 61 0 0 34.448247 39.906518 62 0 0 34.448393 39.906168 63 0 0 34.461012 39.915641 64 0 0 34.466543 39.918932 65 0 0 34.476684 39.928556 66 0 0 34.48306 39.933094 67 0 0 34.502462 39.945626 68 0 0 34.485343 39.931659 69 0 0 34.494559 39.938285 70 0 0 34.498105 39.940098 71 0 0 34.503791 39.946151 72 0 0 34.512159 39.951259 73 0 0 34.51227 39.951813 74 0 0 34.524493 39.959699 75 0 0 34.51833 39.954666 76 0 0 34.519147 39.956736 77 0 0 34.529249 39.961308 78 0 0 34.524654 39.961179 79 0 0 34.535527 39.966486 80 0 0 34.532303 39.964262 81 0 0 34.53337 39.96559 82 0 0 34.532962 39.963295 83 0 0 34.544098 39.972171 84 0 0 34.550234 39.977353 85 0 0 34.548768 39.975654 86 0 0 34.553735 39.979006 87 0 0 34.556236 39.982571 88 0 0 34.555864 39.983466 89 0 0 34.559022 39.982279 90 0 0 34.560964 39.982826 91 0 0 34.562304 39.986711 92 0 0 34.566641 39.98714 93 0 0 34.563618 39.984086 94 0 0 34.566804 39.989291 95 0 0 34.567371 39.988269 96 0 0 34.573337 39.992919 97 0 0 34.579481 39.996058 98 0 0 34.57872 39.996168 99 0 0 34.569985 39.990359 100 0 0 34.573855 39.991764 101 0 0 34.578048 39.996501 102 0 0 34.586722 40.002337 103 0 0 34.594154 40.007192 104 0 0 34.579552 39.996012 105 0 0 34.582359 39.999652 106 0 0 34.595608 40.00861 107 0 0 34.589006 40.004815 108 0 0 34.600924 40.013307 109 0 0 34.594246 40.009168 110 0 0 34.599036 40.008933 111 0 0 34.60433 40.013649 112 0 0 34.609504 40.018758 113 0 0 34.602732 40.01325 114 0 0 34.611063 40.017393 115 0 0 34.606842 40.017525 116 0 0 34.599377 40.012088 117 0 0 34.60731 40.018619 118 0 0 34.610527 40.01902 119 0 0 34.613543 40.02227 120 0 0 34.605689 40.016499 121 0 0 34.616987 40.024553 122 0 0 34.615106 40.02564 123 0 0 34.617889 40.025894 124 0 0 34.618383 40.023145 125 0 0 34.61759 40.026894 126 0 0 34.622527 40.028378 127 0 0 34.627255 40.034666 128 0 0 34.62306 40.02699 129 0 0 34.630536 40.036334 130 0 0 34.631486 40.0363 131 0 0 34.622873 40.028437 132 0 0 34.627042 40.035201 133 0 0 34.633401 40.038303 134 0 0 34.633481 40.038333 135 0 0 34.637938 40.03958 136 0 0 34.637967 40.043162 137 0 0 34.637578 40.041674 138 0 0 34.636234 40.042138 139 0 0 34.645437 40.050407 140 0 0 34.65072 40.05068 141 0 0 34.642105 40.049371 142 0 0 34.649618 40.053305 143 0 0 34.646853 40.051273 144 0 0 34.660632 40.0594 145 0 0 34.657786 40.059578 146 0 0 34.651833 40.054643 147 0 0 34.657817 40.060214 148 0 0 34.660253 40.063197 149 0 0 34.658747 40.06098 150 0 0 34.651238 40.056137 151 0 0 34.657284 40.059013 152 0 0 34.655509 40.062197 153 0 0 34.662681 40.067104 154 0 0 34.663548 40.065233 155 0 0 34.659131 40.064109 156 0 0 34.665586 40.069084 157 0 0 34.672274 40.073464 158 0 0 34.666656 40.068162 159 0 0 34.669649 40.070943 160 0 0 34.670836 40.071583 161 0 0 34.665364 40.071248 162 0 0 34.671841 40.075407 163 0 0 34.676028 40.078279 164 0 0 34.674189 40.076359 165 0 0 34.676722 40.078506 166 0 0 34.678616 40.081872 167 0 0 34.674944 40.080153 168 0 0 34.681008 40.084383 169 0 0 34.681449 40.084924 170 0 0 34.683536 40.085657 171 0 0 34.687297 40.08748 172 0 0 34.683687 40.088184 173 0 0 34.697277 40.097233 174 0 0 34.687807 40.089838 175 0 0 34.689642 40.093096 176 0 0 34.685652 40.090238 177 0 0 34.697082 40.096806 178 0 0 34.699233 40.100912 179 0 0 34.698504 40.100808 180 0 0 34.697009 40.103304 181 0 0 34.697568 40.103475 182 0 0 34.705871 40.110594 183 0 0 34.701691 40.106445 184 0 0 34.714323 40.11506 185 0 0 34.702855 40.110954 186 0 0 34.700378 40.106936 187 0 0 34.714795 40.121035 188 0 0 34.713319 40.120081 189 0 0 34.712774 40.115947 190 0 0 34.712789 40.121309 191 0 0 34.714342 40.122726 192 0 0 34.715045 40.123388 193 0 0 34.710719 40.122661 194 0 0 34.707763 40.121018 195 0 0 34.715052 40.124857 196 0 0 34.698008 40.115904 197 0 0 34.702445 40.119346 198 0 0 34.706506 40.121343 199 0 0 34.701746 40.11826 200 0 0 34.698457 40.117177 201 0 0 34.698569 40.120107 202 0 0 34.697266 40.117701 203 0 0 34.698015 40.119751 204 0 0 34.688452 40.111209 205 0 0 34.690528 40.115827 206 0 0 34.683694 40.11299 207 0 0 34.688824 40.116399 208 0 0 34.66741 40.102809 209 0 0 34.674728 40.10601 210 0 0 34.662914 40.096548 211 0 0 34.671673 40.107169 212 0 0 34.672808 40.105768 213 0 0 34.64371 40.082816 214 0 0 34.642377 40.085161 215 0 0 34.638899 40.086537 216 0 0 34.621315 40.071887 217 0 0 34.625533 40.07099 218 0 0 34.617148 40.070339 219 0 0 34.603275 40.060961 220 0 0 34.60578 40.061894 221 0 0 34.597275 40.056563 222 0 0 34.581626 40.045502 223 0 0 34.576587 40.040097 224 0 0 34.566976 40.038307 225 0 0 34.559836 40.03079 226 0 0 34.553728 40.029849 227 0 0 34.53475 40.014462 228 0 0 34.509906 39.995958 229 0 0 34.507773 39.997332 230 0 0 34.501522 39.990763 231 0 0 34.50104 39.991069 232 0 0 34.483709 39.982996 233 0 0 34.470246 39.972381 234 0 0 34.466184 39.970222 235 0 0 34.438803 39.945624 236 0 0 34.426756 39.939262 237 0 0 34.424964 39.939417 238 0 0 34.412786 39.929404 239 0 0 34.414204 39.93229 240 0 0 34.381611 39.909921 241 0 0 34.37473 39.906918 242 0 0 34.354621 39.89084 243 0 0 34.342985 39.879807 244 0 0 34.316664 39.865028 245 0 0 34.321065 39.870281 246 0 0 34.297185 39.851173 247 0 0 34.277285 39.839253 248 0 0 34.250683 39.821202 249 0 0 34.253312 39.820784 250 0 0 34.226945 39.804305 251 0 0 34.226179 39.801803 252 0 0 34.194281 39.783159 253 0 0 34.175489 39.769565 254 0 0 34.170425 39.766888 255 0 0 34.151532 39.752032 256 0 0 34.127723 39.737713 257 0 0 34.124874 39.734018 258 0 0 34.092155 39.711489 259 0 0 34.094245 39.711857 260 0 0 34.06983 39.694691 261 0 0 34.03184 39.672219 262 0 0 34.020363 39.662586 263 0 0 33.999622 39.648513 264 0 0 33.9866 39.637696 265 0 0 33.961866 39.623481 266 0 0 33.94348 39.609235 267 0 0 33.926615 39.600796 268 0 0 33.917187 39.593182 269 0 0 33.87939 39.56448 270 0 0 33.838663 39.540048 271 0 0 33.834692 39.538665 272 0 0 33.803143 39.52063 273 0 0 33.79193 39.507066 274 0 0 33.759428 39.482525 275 0 0 33.751043 39.479889 276 0 0 33.697486 39.444062 277 0 0 33.678407 39.431448 278 0 0 33.662413 39.41668 279 0 0 33.646909 39.402441 280 0 0 33.613534 39.394176 281 0 0 33.557755 39.352732 282 0 0 33.543094 39.339925 283 0 0 33.504077 39.311962 284 0 0 33.487092 39.303926 285 0 0 33.461751 39.293227 286 0 0 33.418451 39.254337 287 0 0 33.417381 39.25481 288 0 0 33.398583 39.245451 289 0 0 33.353086 39.218615 290 0 0 33.323772 39.198365 291 0 0 33.315456 39.183947 292 0 0 33.276713 39.161307 293 0 0 33.227455 39.128931 294 0 0 33.224447 39.131483 295 0 0 33.19646 39.113163 296 0 0 33.202921 39.114212 297 0 0 33.186425 39.112293 298 0 0 33.114652 39.063062 299 0 0 33.113848 39.054954 300 0 0 33.0318 38.998302 301 0 0 33.082871 39.028608 302 0 0 33.016913 38.993802 303 0 0 32.95488 38.947642 304 0 0 32.950511 38.942926 305 0 0 33.037059 39.017373 306 0 0 32.885022 38.907968 307 0 0 32.948474 38.934861 308 0 0 32.870104 38.892093 309 0 0 32.805218 38.861699 310 0 0 32.895216 38.92425 311 0 0 32.75084 38.809787 312 0 0 32.781939 38.834933 313 0 0 32.785461 38.846421 314 0 0 32.769947 38.845185 315 0 0 32.620015 38.73595 316 0 0 32.755382 38.826962 317 0 0 32.68173 38.78492 318 0 0 32.750023 38.839008 319 0 0 32.661736 38.777268 320 0 0 32.741625 38.803369 321 0 0 32.647044 38.767765 322 0 0 32.749207 38.820409 323 0 0 32.614481 38.771521 324 0 0 32.680913 38.808584 325 0 0 32.576798 38.706826 326 0 0 32.581877 38.770086 327 0 0 32.654888 38.755997 328 0 0 32.689177 38.779317 329 0 0 32.755964 38.831829 330 0 0 32.601805 38.71769 331 0 0 32.589712 38.711354 332 0 0 32.620909 38.740152 333 0 0 32.876915 38.952673 334 0 0 32.459584 38.694573 335 0 0 32.522368 38.678289 336 0 0 32.494853 38.723775 337 0 0 32.547185 38.754691 338 0 0 32.630784 38.696569 339 0 0 32.341489 38.620213 340 0 0 33.086348 39.128355 341 0 0 32.659603 38.8883 342 0 0 32.662281 38.773392 343 0 0 32.943987 39.010434 344 0 0 32.775629 38.715023 345 0 0 32.733189 38.807664 346 0 0 33.25 39.135522 347 0 0 32.561111 38.814815 348 0 0 32.617284 38.683128 349 0 0 32.054422 38.371882 350 0 0 33 38.94186 351 0 0 33.017467 39.049491 352 0 0 32.970588 38.931373 353 0 0 32.21978 38.342491 354 0 0 32.339286 38.710317 355 0 0 33.038961 39.199134 356 0 0 32.88189 38.992126 357 0 0 33.84466 39.462783 358 0 0 32.655914 38.598566 359 0 0 33.141176 39.137255 360 0 0 32.907895 39.030702 361 0 0 32.776119 39.029851 362 0 0 32.557377 38.863388 363 0 0 32.12963 38.376543 364 0 0 31.88 38.36 365 0 0 32.489362 38.815603 366 0 0 33.04878 39.357724 367 0 0 31.111111 37.638889 368 0 0 33.62069 39.609195 369 0 0 32.692308 39.128205 370 0 0 33.26087 38.855072 371 0 0 31.5 37.683333 372 0 0 29.888889 37.518519 373 0 0 33.611111 39.555556 374 0 0 33.333333 39.066667 375 0 0 28.333333 36.277778 376 0 0 35 40.233333 377 0 0 28.2 34.6 378 0 0 33.777778 39.222222 379 0 0 26.142857 33.095238 380 0 0 36 40.904762 381 0 0 36 41 382 0 0 36 41 383 0 0 33 38.833333 384 0 0 36 41 385 0 0 32.25 38.333333 386 0 0 34.666667 40.111111 387 0 0 31.666667 36.666667 388 0 0 36 41 389 0 0 36 41 390 0 0 32.5 39 391 0 0 36 41 392 0 0 36 41 393 0 0 27 35.166667 394 0 0 36 41 395 0 0 36 40.666667 396 0 0 36 41 397 0 0 32.5 39 398 0 0 31.5 38.166667 399 0 0 33.5 39.166667 400 0 0 36 40.666667 401 0 0 21 29.666667 402 0 0 36 41 403 0 0 20 24 404 0 0 36 41 405 0 0 26 33 406 0 0 31 38 407 0 0 31 38 408 0 0 23 35 409 0 0 31 38 410 0 0 31 38 411 0 0 8 21.666667 412 0 0 32 37 413 0 0 32 37 414 0 0 29 37 415 0 0 26 36 416 0 0 36 41 417 0 0 26 36 418 0 0 36 41 419 0 0 36 41 420 0 0 26 36 421 0 0 11 27.666667 422 0 0 36 41 423 0 0 36 41 424 0 0 36 41 425 0 0 36 41 426 0 0 11 31 427 0 0 26 36 428 0 0 36 41 429 0 0 7 21.666667 430 0 0 18 27.666667 431 0 0 36 41 432 0 0 36 40.333333 433 0 0 36 41 434 0 0 7 16.333333 435 0 0 36 41 436 0 0 21 30.333333 437 0 0 7 13.333333 438 0 0 36 41 439 0 0 8 21 440 0 0 36 41