## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/data/Runs/415630/output/415630-20250125_0254/415630-L3453-Z0001-CAGCTCGAATGCGAT/415630-L3453-Z0001-CAGCTCGAATGCGAT_sample.recal.bam OUTPUT=/data/Runs/415630/output/415630-20250125_0254/415630-L3453-Z0001-CAGCTCGAATGCGAT/415630-L3453-Z0001-CAGCTCGAATGCGAT_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 12:31:06 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 745099 745099 231 172218116 172218116 167586744 167586744 156781136 156781136 0 0 0.973108 0.910364 0 0.973108 0.910364 0 516654348 516654348 511144923 511144923 495056522 495056522 469032875 469032875 0.989336 0.958197 0.907827 0.989336 0.958197 0.907827 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 1346 2 35.171489 40.349988 1 20239 10 32.432587 38.657087 2 26203 15045 33.462306 39.232697 3 52745 3546 33.714294 39.392827 4 69452 83755 33.769725 39.426852 5 174068 15497 33.77855 39.437097 6 63117 217975 33.80185 39.455513 7 250891 244543 33.822229 39.468587 8 107991 144757 33.850429 39.486887 9 210875 141407 33.859509 39.495699 10 246886 410568 33.891366 39.516098 11 273957 100538 33.892881 39.517308 12 315067 532307 33.905585 39.526315 13 221036 203221 33.941444 39.553292 14 505539 711620 33.976753 39.576615 15 396156 477196 33.986861 39.584285 16 273014 173299 34.003129 39.597076 17 527088 755488 34.019379 39.609661 18 556258 920618 34.040733 39.622061 19 339444 358033 34.050473 39.630527 20 810950 766389 34.059563 39.634618 21 758214 1502021 34.087976 39.65495 22 455673 337290 34.108282 39.667835 23 1756272 2218155 34.118905 39.678008 24 706792 1170688 34.134782 39.690766 25 624815 528256 34.15136 39.701425 26 2014328 3267939 34.173168 39.714802 27 490869 1091196 34.184896 39.724921 28 799926 744385 34.189257 39.726094 29 2387769 4462082 34.205851 39.738871 30 798524 115487 34.215345 39.743432 31 2367865 1619471 34.232293 39.756413 32 3202563 3454826 34.239727 39.762764 33 842527 426141 34.252532 39.774778 34 2832190 5658936 34.258957 39.778132 35 2392757 2158691 34.271434 39.78788 36 144344710 4461322 34.291125 39.802998 37 0 2588599 34.295539 39.803897 38 0 838719 34.303043 39.808865 39 0 4701455 34.325366 39.824085 40 0 15 34.338768 39.83403 41 0 469032860 34.353756 39.84376 42 0 0 34.361256 39.848482 43 0 0 34.368406 39.852234 44 0 0 34.37295 39.856584 45 0 0 34.395032 39.873261 46 0 0 34.399339 39.876686 47 0 0 34.406173 39.880375 48 0 0 34.426782 39.897058 49 0 0 34.419908 39.890354 50 0 0 34.431864 39.896153 51 0 0 34.442578 39.906902 52 0 0 34.460542 39.916968 53 0 0 34.463362 39.920588 54 0 0 34.474486 39.9272 55 0 0 34.490006 39.938782 56 0 0 34.494609 39.940507 57 0 0 34.495982 39.943553 58 0 0 34.501611 39.946026 59 0 0 34.502681 39.947712 60 0 0 34.511837 39.953062 61 0 0 34.522543 39.959453 62 0 0 34.532288 39.967668 63 0 0 34.530246 39.965599 64 0 0 34.544045 39.975461 65 0 0 34.542665 39.976303 66 0 0 34.557231 39.984565 67 0 0 34.55936 39.987274 68 0 0 34.572556 39.993979 69 0 0 34.567339 39.992522 70 0 0 34.578137 39.99828 71 0 0 34.580799 40.002753 72 0 0 34.579727 40.000888 73 0 0 34.582635 40.003296 74 0 0 34.594963 40.009738 75 0 0 34.591051 40.009406 76 0 0 34.59373 40.00854 77 0 0 34.605192 40.015158 78 0 0 34.620003 40.027873 79 0 0 34.601716 40.016282 80 0 0 34.606687 40.018976 81 0 0 34.612288 40.022314 82 0 0 34.616336 40.026713 83 0 0 34.614882 40.025756 84 0 0 34.624589 40.033952 85 0 0 34.622775 40.031287 86 0 0 34.622098 40.029207 87 0 0 34.625313 40.033893 88 0 0 34.629619 40.036107 89 0 0 34.622685 40.030555 90 0 0 34.633476 40.037831 91 0 0 34.637655 40.040768 92 0 0 34.63363 40.03682 93 0 0 34.639141 40.041526 94 0 0 34.630035 40.034737 95 0 0 34.644041 40.043925 96 0 0 34.639667 40.040881 97 0 0 34.655823 40.052651 98 0 0 34.644927 40.04441 99 0 0 34.661238 40.055848 100 0 0 34.653198 40.051699 101 0 0 34.654402 40.051648 102 0 0 34.654185 40.053209 103 0 0 34.663323 40.05775 104 0 0 34.660906 40.055059 105 0 0 34.654481 40.051422 106 0 0 34.658346 40.054156 107 0 0 34.661866 40.057328 108 0 0 34.659945 40.056083 109 0 0 34.655736 40.051911 110 0 0 34.661105 40.057312 111 0 0 34.663263 40.05757 112 0 0 34.664272 40.059948 113 0 0 34.67349 40.064752 114 0 0 34.670831 40.062531 115 0 0 34.668631 40.062553 116 0 0 34.676868 40.066669 117 0 0 34.674014 40.064535 118 0 0 34.673999 40.065432 119 0 0 34.68473 40.07458 120 0 0 34.676332 40.066987 121 0 0 34.676962 40.065666 122 0 0 34.682223 40.073163 123 0 0 34.684041 40.073503 124 0 0 34.684715 40.072852 125 0 0 34.679301 40.070315 126 0 0 34.682294 40.072575 127 0 0 34.689294 40.076934 128 0 0 34.680151 40.073555 129 0 0 34.685046 40.075985 130 0 0 34.681575 40.072928 131 0 0 34.679824 40.072483 132 0 0 34.691887 40.082539 133 0 0 34.687588 40.078202 134 0 0 34.695588 40.082605 135 0 0 34.687253 40.0779 136 0 0 34.697276 40.084222 137 0 0 34.706161 40.089144 138 0 0 34.701213 40.086858 139 0 0 34.694846 40.081433 140 0 0 34.69942 40.088876 141 0 0 34.691448 40.080662 142 0 0 34.691193 40.081615 143 0 0 34.698575 40.086594 144 0 0 34.707281 40.094821 145 0 0 34.70546 40.093415 146 0 0 34.699016 40.090596 147 0 0 34.70236 40.091327 148 0 0 34.705528 40.092237 149 0 0 34.706341 40.093532 150 0 0 34.709905 40.097079 151 0 0 34.709726 40.097935 152 0 0 34.710943 40.097099 153 0 0 34.699631 40.089967 154 0 0 34.705674 40.09552 155 0 0 34.702102 40.092031 156 0 0 34.702537 40.09419 157 0 0 34.709107 40.100879 158 0 0 34.707681 40.097494 159 0 0 34.709392 40.099799 160 0 0 34.708464 40.099139 161 0 0 34.727762 40.112175 162 0 0 34.715814 40.104856 163 0 0 34.724326 40.111848 164 0 0 34.720462 40.109467 165 0 0 34.708545 40.102315 166 0 0 34.722992 40.109919 167 0 0 34.727497 40.11125 168 0 0 34.717951 40.106678 169 0 0 34.722997 40.111358 170 0 0 34.723889 40.112638 171 0 0 34.718697 40.109792 172 0 0 34.725141 40.114734 173 0 0 34.723376 40.114589 174 0 0 34.719017 40.110438 175 0 0 34.727706 40.118362 176 0 0 34.720177 40.1134 177 0 0 34.724224 40.118592 178 0 0 34.723613 40.116788 179 0 0 34.727651 40.121125 180 0 0 34.724304 40.120754 181 0 0 34.726959 40.122796 182 0 0 34.732916 40.127062 183 0 0 34.726486 40.12202 184 0 0 34.729193 40.126351 185 0 0 34.728471 40.125452 186 0 0 34.724261 40.123386 187 0 0 34.727474 40.126512 188 0 0 34.725008 40.124982 189 0 0 34.728423 40.12684 190 0 0 34.734283 40.130643 191 0 0 34.727752 40.12814 192 0 0 34.720271 40.126007 193 0 0 34.724659 40.127629 194 0 0 34.727127 40.13137 195 0 0 34.726687 40.132524 196 0 0 34.717242 40.126477 197 0 0 34.720827 40.131637 198 0 0 34.716102 40.127525 199 0 0 34.715045 40.127461 200 0 0 34.719761 40.131298 201 0 0 34.708456 40.124077 202 0 0 34.717134 40.131103 203 0 0 34.720901 40.133712 204 0 0 34.701378 40.119855 205 0 0 34.695258 40.11592 206 0 0 34.684665 40.112337 207 0 0 34.700772 40.123424 208 0 0 34.677847 40.107508 209 0 0 34.679374 40.108728 210 0 0 34.675576 40.106697 211 0 0 34.672643 40.105228 212 0 0 34.671428 40.103504 213 0 0 34.670842 40.105636 214 0 0 34.659152 40.09696 215 0 0 34.659906 40.095324 216 0 0 34.648093 40.087262 217 0 0 34.633165 40.077965 218 0 0 34.626776 40.07782 219 0 0 34.620572 40.074486 220 0 0 34.617633 40.069887 221 0 0 34.596233 40.05446 222 0 0 34.594543 40.052466 223 0 0 34.599815 40.060076 224 0 0 34.572997 40.040508 225 0 0 34.571484 40.038331 226 0 0 34.550536 40.023715 227 0 0 34.550049 40.024378 228 0 0 34.535301 40.015797 229 0 0 34.534965 40.013834 230 0 0 34.526933 40.011235 231 0 0 34.514431 40.00208 232 0 0 34.505753 39.995487 233 0 0 34.487052 39.983534 234 0 0 34.479855 39.976914 235 0 0 34.47324 39.973019 236 0 0 34.45599 39.95901 237 0 0 34.448073 39.951979 238 0 0 34.430096 39.945648 239 0 0 34.416487 39.934256 240 0 0 34.379836 39.91115 241 0 0 34.398825 39.921567 242 0 0 34.384273 39.90991 243 0 0 34.359341 39.893168 244 0 0 34.351197 39.891308 245 0 0 34.34258 39.881007 246 0 0 34.318752 39.867331 247 0 0 34.30718 39.858333 248 0 0 34.290496 39.85002 249 0 0 34.251549 39.823463 250 0 0 34.244635 39.819055 251 0 0 34.234147 39.809147 252 0 0 34.220942 39.796046 253 0 0 34.217959 39.796604 254 0 0 34.195518 39.783943 255 0 0 34.180058 39.768536 256 0 0 34.160477 39.755971 257 0 0 34.137849 39.743464 258 0 0 34.117995 39.726517 259 0 0 34.1046 39.722124 260 0 0 34.090836 39.710669 261 0 0 34.04837 39.682732 262 0 0 34.051413 39.680419 263 0 0 34.013549 39.6552 264 0 0 33.993818 39.642645 265 0 0 33.975987 39.629791 266 0 0 33.944635 39.613265 267 0 0 33.939368 39.604593 268 0 0 33.894562 39.575097 269 0 0 33.883488 39.5649 270 0 0 33.867137 39.557827 271 0 0 33.850504 39.544471 272 0 0 33.807846 39.519289 273 0 0 33.791533 39.506626 274 0 0 33.760691 39.485189 275 0 0 33.737957 39.470486 276 0 0 33.716833 39.454026 277 0 0 33.690249 39.437148 278 0 0 33.663609 39.417505 279 0 0 33.634573 39.398302 280 0 0 33.600643 39.379095 281 0 0 33.57807 39.367509 282 0 0 33.550551 39.343542 283 0 0 33.524579 39.321348 284 0 0 33.516605 39.318256 285 0 0 33.444692 39.264281 286 0 0 33.43894 39.268605 287 0 0 33.404347 39.244967 288 0 0 33.384096 39.238591 289 0 0 33.35667 39.209053 290 0 0 33.323644 39.190393 291 0 0 33.310243 39.191256 292 0 0 33.30077 39.180509 293 0 0 33.221239 39.120952 294 0 0 33.251464 39.143086 295 0 0 33.203215 39.113731 296 0 0 33.159783 39.080176 297 0 0 33.129285 39.062394 298 0 0 33.147206 39.062333 299 0 0 33.108676 39.052655 300 0 0 33.078384 39.033846 301 0 0 33.046562 39.011153 302 0 0 33.02193 38.984789 303 0 0 32.998318 38.971318 304 0 0 32.986487 38.966288 305 0 0 33.017743 38.994464 306 0 0 32.908127 38.908773 307 0 0 32.867891 38.896805 308 0 0 32.931262 38.918787 309 0 0 32.846171 38.888707 310 0 0 32.775519 38.834481 311 0 0 32.820462 38.855206 312 0 0 32.851421 38.887279 313 0 0 32.742554 38.813855 314 0 0 32.637139 38.734429 315 0 0 32.707173 38.803776 316 0 0 32.754762 38.796974 317 0 0 32.84942 38.892208 318 0 0 32.683807 38.768022 319 0 0 32.747683 38.819668 320 0 0 32.722896 38.828208 321 0 0 32.722201 38.825498 322 0 0 32.75432 38.846897 323 0 0 32.591573 38.718646 324 0 0 32.626412 38.750072 325 0 0 32.633515 38.770598 326 0 0 32.679643 38.792953 327 0 0 32.640117 38.758287 328 0 0 32.552624 38.687679 329 0 0 32.666978 38.804465 330 0 0 32.668651 38.817747 331 0 0 32.703586 38.814741 332 0 0 32.676069 38.773582 333 0 0 32.570329 38.740075 334 0 0 32.875 38.913786 335 0 0 32.919376 38.912007 336 0 0 32.534917 38.763619 337 0 0 32.624697 38.782351 338 0 0 32.821265 38.881454 339 0 0 32.707645 38.875689 340 0 0 32.590106 38.773459 341 0 0 33.035573 39.013614 342 0 0 32.631657 38.768738 343 0 0 32.657095 38.822072 344 0 0 32.389734 38.702155 345 0 0 32.537473 38.754461 346 0 0 33.156398 39.124803 347 0 0 32.662234 38.838652 348 0 0 32.132931 38.563948 349 0 0 32.52 38.725556 350 0 0 32.301115 38.636927 351 0 0 32.92887 38.916318 352 0 0 32.876777 39.045814 353 0 0 32.097826 38.521739 354 0 0 32.447853 38.554192 355 0 0 33.208633 39.1247 356 0 0 33.079365 39.02381 357 0 0 32.486957 38.753623 358 0 0 33.048544 39.28479 359 0 0 33.755556 39.655556 360 0 0 33.493671 39.303797 361 0 0 32.855263 39.013158 362 0 0 32.984615 39.215385 363 0 0 32.796296 38.839506 364 0 0 31.729167 38.340278 365 0 0 33.785714 39.261905 366 0 0 34 39.491228 367 0 0 34.324324 39.828829 368 0 0 32.741935 38.806452 369 0 0 33.962963 39.888889 370 0 0 34.346154 39.961538 371 0 0 33.521739 39.333333 372 0 0 32.45 39.15 373 0 0 34.722222 40.277778 374 0 0 36 41 375 0 0 34.428571 39.738095 376 0 0 33.357143 39.166667 377 0 0 33.923077 39.615385 378 0 0 33.583333 39.444444 379 0 0 33 38.424242 380 0 0 35.363636 40.454545 381 0 0 34 39.555556 382 0 0 32.75 39.166667 383 0 0 29.875 37.416667 384 0 0 34.571429 39.857143 385 0 0 29.571429 36.571429 386 0 0 31.857143 38.904762 387 0 0 35.166667 40.5 388 0 0 31.166667 37.888889 389 0 0 36 41 390 0 0 26 33.466667 391 0 0 35 40.4 392 0 0 36 41 393 0 0 34.666667 40.222222 394 0 0 31.333333 38.555556 395 0 0 36 41 396 0 0 33 39.166667 397 0 0 35.5 40.5 398 0 0 36 41 399 0 0 36 41