## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5289-Z0034-CTGTGAATATGCGAT/441525-L5289-Z0034-CTGTGAATATGCGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5289-Z0034-CTGTGAATATGCGAT/441525-L5289-Z0034-CTGTGAATATGCGAT_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 03:00:00 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 999282 999282 137 137834030 137834030 133147871 133147871 123996663 123996663 0 0 0.966001 0.899608 0 0.966001 0.899608 0 413502090 413502090 407301978 407301978 392784978 392784978 368093414 368093414 0.985006 0.949898 0.890185 0.985006 0.949898 0.890185 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 717 0 35.990901 40.992748 1 9271 0 35.984212 40.988553 2 11791 3760 35.995112 40.995844 3 29135 1093 35.982787 40.985663 4 49075 39941 35.989757 40.991179 5 96857 15419 35.994244 40.995274 6 103638 104990 35.977141 40.98146 7 175247 138703 35.977941 40.984449 8 187685 137723 35.987451 40.9897 9 225618 93392 35.959603 40.965914 10 232824 476738 35.87142 40.925067 11 280307 52181 35.914679 40.935881 12 336469 673617 35.224352 40.346199 13 345970 193454 33.685619 39.565207 14 438295 956106 35.882821 40.928657 15 355116 356484 35.827523 40.880149 16 379874 435209 35.805173 40.827212 17 511840 1109232 35.909092 40.922007 18 543873 701997 35.735531 40.784591 19 372557 710073 35.785228 40.839378 20 496638 1009744 35.921342 40.945115 21 653214 1340547 35.82364 40.868501 22 320266 567077 35.608242 40.735874 23 1016046 1184535 35.261762 40.469184 24 574800 1158602 35.368805 40.564967 25 545156 486836 35.402364 40.593916 26 1757033 2465682 35.320989 40.521487 27 355041 861809 35.359011 40.565271 28 957034 377149 35.357395 40.564452 29 2475980 5065019 35.34267 40.550482 30 763764 39167 35.392561 40.584718 31 2378204 801165 35.389111 40.580648 32 1579215 5438878 35.363362 40.55615 33 842959 115895 35.387821 40.581009 34 2464095 2591848 35.389547 40.584312 35 2266458 3879234 35.40814 40.597232 36 113701968 2031309 35.427981 40.611847 37 0 4345702 35.42625 40.611837 38 0 370844 35.42528 40.611266 39 0 5077522 35.420319 40.605306 40 0 1 35.412266 40.600345 41 0 368093413 35.406336 40.594594 42 0 0 35.401463 40.59228 43 0 0 35.405724 40.59534 44 0 0 35.415595 40.601212 45 0 0 35.414538 40.602292 46 0 0 35.403551 40.592543 47 0 0 35.395318 40.585331 48 0 0 35.374767 40.572616 49 0 0 35.380773 40.575353 50 0 0 35.386566 40.582111 51 0 0 35.383018 40.578369 52 0 0 35.335432 40.546858 53 0 0 35.308378 40.53703 54 0 0 35.318217 40.542791 55 0 0 35.31102 40.536997 56 0 0 35.263099 40.513786 57 0 0 35.314873 40.534449 58 0 0 35.293375 40.51556 59 0 0 35.268967 40.496183 60 0 0 35.235216 40.471671 61 0 0 35.19385 40.441703 62 0 0 35.146095 40.405412 63 0 0 35.100448 40.369847 64 0 0 35.052557 40.33129 65 0 0 34.989195 40.286117 66 0 0 34.922112 40.237392 67 0 0 34.844859 40.178675 68 0 0 34.765722 40.120118 69 0 0 34.680008 40.054665 70 0 0 34.578371 39.975887 71 0 0 34.479995 39.897559 72 0 0 34.378915 39.816158 73 0 0 34.279998 39.738848 74 0 0 34.18181 39.658799 75 0 0 34.091803 39.59291 76 0 0 34.001705 39.522976 77 0 0 33.906723 39.451867 78 0 0 33.832728 39.394741 79 0 0 33.765555 39.34136 80 0 0 33.693719 39.280422 81 0 0 33.641025 39.24002 82 0 0 33.587685 39.195608 83 0 0 33.533443 39.151898 84 0 0 33.49854 39.124226 85 0 0 33.463443 39.096012 86 0 0 33.4315 39.067285 87 0 0 33.386481 39.029538 88 0 0 33.33407 38.986932 89 0 0 33.283298 38.943196 90 0 0 33.249044 38.91352 91 0 0 33.207416 38.874129 92 0 0 33.164918 38.83901 93 0 0 33.148616 38.826678 94 0 0 33.10734 38.789055 95 0 0 33.081029 38.769164 96 0 0 33.063089 38.755265 97 0 0 33.067626 38.754669 98 0 0 33.068337 38.755707 99 0 0 33.089935 38.769141 100 0 0 33.119441 38.794525 101 0 0 33.160312 38.826692 102 0 0 33.19522 38.850901 103 0 0 33.219587 38.871273 104 0 0 33.238185 38.881625 105 0 0 33.242718 38.881306 106 0 0 33.233122 38.872295 107 0 0 33.226188 38.863494 108 0 0 33.193659 38.84015 109 0 0 33.167403 38.81824 110 0 0 33.132851 38.78773 111 0 0 33.066139 38.738164 112 0 0 33.013131 38.696786 113 0 0 32.955014 38.648932 114 0 0 32.902069 38.60324 115 0 0 32.846742 38.558102 116 0 0 32.806806 38.527899 117 0 0 32.797988 38.525033 118 0 0 32.787827 38.515429 119 0 0 32.786136 38.51771 120 0 0 32.804397 38.531539 121 0 0 32.798157 38.525586 122 0 0 32.79768 38.522061 123 0 0 32.805149 38.528763 124 0 0 32.800519 38.521061 125 0 0 32.818564 38.528555 126 0 0 32.819877 38.528072 127 0 0 32.801815 38.506001 128 0 0 32.780748 38.486594 129 0 0 32.756385 38.466982 130 0 0 32.709691 38.427745 131 0 0 32.682212 38.405445 132 0 0 32.664913 38.386758 133 0 0 32.660081 38.384509 134 0 0 32.662207 38.38423 135 0 0 32.632056 38.359222 136 0 0 32.643439 38.368439 137 0 0 32.635217 38.363035 138 0 0 32.632969 38.357644 139 0 0 32.657352 38.38314 140 0 0 32.689114 38.40558 141 0 0 32.686219 38.404625 142 0 0 32.722483 38.432373 143 0 0 32.714765 38.42452 144 0 0 32.710103 38.418459 145 0 0 32.696451 38.408147 146 0 0 32.671909 38.384515 147 0 0 32.639891 38.354942 148 0 0 32.610707 38.327076 149 0 0 32.574307 38.302578 150 0 0 32.529085 38.263234 151 0 0 32.505497 38.243688 152 0 0 32.486504 38.22844 153 0 0 32.505068 38.24144 154 0 0 32.505749 38.245942 155 0 0 32.500107 38.239411 156 0 0 32.519908 38.259043 157 0 0 32.563236 38.294681 158 0 0 32.608544 38.330476 159 0 0 32.646446 38.357509 160 0 0 32.675282 38.377229 161 0 0 32.718649 38.413644 162 0 0 32.772033 38.460063 163 0 0 32.778488 38.458097 164 0 0 32.810339 38.487549 165 0 0 32.834175 38.504929 166 0 0 32.826896 38.498838 167 0 0 32.847014 38.509551 168 0 0 32.812496 38.475877 169 0 0 32.76871 38.442716 170 0 0 32.757449 38.434712 171 0 0 32.763806 38.436881 172 0 0 32.768966 38.443879 173 0 0 32.782102 38.457635 174 0 0 32.781668 38.467869 175 0 0 32.827408 38.502098 176 0 0 32.855006 38.526018 177 0 0 32.880493 38.554803 178 0 0 32.9352 38.589938 179 0 0 33.007908 38.653969 180 0 0 33.041988 38.682357 181 0 0 33.082983 38.719508 182 0 0 33.133364 38.761963 183 0 0 33.15406 38.785098 184 0 0 33.177179 38.799034 185 0 0 33.175154 38.8028 186 0 0 33.209443 38.832249 187 0 0 33.264331 38.868585 188 0 0 33.256891 38.873774 189 0 0 33.258799 38.875285 190 0 0 33.253812 38.869008 191 0 0 33.273548 38.888047 192 0 0 33.255356 38.875524 193 0 0 33.221842 38.856656 194 0 0 33.185059 38.835069 195 0 0 33.182566 38.83596 196 0 0 33.210681 38.863706 197 0 0 33.206238 38.861924 198 0 0 33.236917 38.888307 199 0 0 33.209137 38.880671 200 0 0 33.223301 38.898091 201 0 0 33.188374 38.874893 202 0 0 33.194638 38.885765 203 0 0 33.196347 38.899372 204 0 0 33.196063 38.895139 205 0 0 33.171208 38.893243 206 0 0 33.170787 38.8889 207 0 0 33.182985 38.89487 208 0 0 33.125691 38.863057 209 0 0 33.082387 38.837893 210 0 0 33.096498 38.849767 211 0 0 33.079699 38.844844 212 0 0 33.044136 38.825419 213 0 0 33.04816 38.825386 214 0 0 32.987179 38.78373 215 0 0 32.986907 38.790668 216 0 0 32.980581 38.77312 217 0 0 32.99845 38.794084 218 0 0 32.901671 38.732042 219 0 0 32.88718 38.722308 220 0 0 32.915772 38.746261 221 0 0 32.855902 38.702395 222 0 0 32.862311 38.709686 223 0 0 32.82794 38.679857 224 0 0 32.81119 38.683043 225 0 0 32.76775 38.648091 226 0 0 32.733587 38.636841 227 0 0 32.733193 38.628514 228 0 0 32.743162 38.638281 229 0 0 32.698172 38.612315 230 0 0 32.727918 38.623193 231 0 0 32.643364 38.579332 232 0 0 32.542368 38.511016 233 0 0 32.619881 38.577208 234 0 0 32.590536 38.548134 235 0 0 32.56443 38.535855 236 0 0 32.557039 38.52041 237 0 0 32.566211 38.535727 238 0 0 32.546489 38.507392 239 0 0 32.443567 38.444915 240 0 0 32.362481 38.391969 241 0 0 32.45088 38.469784 242 0 0 32.41094 38.428083 243 0 0 32.346534 38.3811 244 0 0 32.318935 38.358048 245 0 0 32.325379 38.374909 246 0 0 32.247078 38.315401 247 0 0 32.211836 38.310174 248 0 0 32.142829 38.25601 249 0 0 32.109804 38.230165 250 0 0 32.115379 38.247868 251 0 0 32.077806 38.227089 252 0 0 31.985057 38.154446 253 0 0 32.011857 38.186183 254 0 0 32.022068 38.173138 255 0 0 31.908202 38.111111 256 0 0 31.885632 38.094692 257 0 0 31.794292 38.035761 258 0 0 31.792039 38.040418 259 0 0 31.807935 38.058523 260 0 0 31.752125 38.001129 261 0 0 31.717387 37.998888 262 0 0 31.62877 37.951784 263 0 0 31.509365 37.841109 264 0 0 31.323937 37.731329 265 0 0 31.373371 37.772588 266 0 0 31.387008 37.768578 267 0 0 31.361301 37.755742 268 0 0 31.218161 37.654811 269 0 0 31.090586 37.584763 270 0 0 31.209596 37.6371 271 0 0 31.081432 37.564621 272 0 0 30.969236 37.48954 273 0 0 30.961751 37.487726 274 0 0 30.900803 37.446799 275 0 0 30.697589 37.29803 276 0 0 30.769197 37.374867 277 0 0 30.575273 37.227303 278 0 0 30.549322 37.196792 279 0 0 30.5369 37.21808 280 0 0 30.400737 37.100605 281 0 0 30.198209 36.975058 282 0 0 30.227236 37.03236 283 0 0 30.186357 36.978768 284 0 0 30.132633 36.94904 285 0 0 30.080219 36.918219 286 0 0 30.149093 36.905955 287 0 0 29.845769 36.714819 288 0 0 29.957379 36.8034 289 0 0 29.816815 36.75966 290 0 0 29.813678 36.692142 291 0 0 29.785685 36.710604 292 0 0 29.587927 36.560342 293 0 0 29.683414 36.604084 294 0 0 29.490555 36.491215 295 0 0 29.318716 36.343978 296 0 0 29.301359 36.347802 297 0 0 29.306228 36.345098 298 0 0 29.216889 36.267412 299 0 0 29.182885 36.317304 300 0 0 29.278959 36.370753 301 0 0 29.103138 36.225802 302 0 0 28.985411 36.096891 303 0 0 29.044258 36.130911 304 0 0 28.961796 36.131977 305 0 0 29.146335 36.235253 306 0 0 28.865481 36.04206 307 0 0 28.758326 35.951763 308 0 0 28.693267 35.907627 309 0 0 29.084672 36.203146 310 0 0 28.777698 36.056469 311 0 0 28.447207 35.775695 312 0 0 28.582336 35.852524 313 0 0 28.513883 35.682386 314 0 0 28.234568 35.626622 315 0 0 28.480427 35.773937 316 0 0 28.307523 35.7203 317 0 0 28.315508 35.636166 318 0 0 27.948387 35.399355 319 0 0 28.19986 35.577685 320 0 0 28.201378 35.591373 321 0 0 28.139594 35.675409 322 0 0 28.024345 35.57397 323 0 0 28.341164 35.717739 324 0 0 28.609234 35.957583 325 0 0 27.708955 35.195688 326 0 0 28.427596 35.869308 327 0 0 27.792227 35.324863 328 0 0 27.828947 35.239583 329 0 0 28.099065 35.652336 330 0 0 28.169421 35.46281 331 0 0 27.610599 35.278034 332 0 0 27.588083 35.136442 333 0 0 27.179941 35.013766 334 0 0 27.359736 35.029703 335 0 0 28.821168 36.064477 336 0 0 27.590717 35.28692 337 0 0 28.458716 35.856269 338 0 0 27.673913 35.226449 339 0 0 26.834395 34.282378 340 0 0 28.240602 35.496241 341 0 0 26.634783 34.463768 342 0 0 26.877358 34.95283 343 0 0 26.548387 34.498208 344 0 0 28.25974 35.593074 345 0 0 28.847222 35.939815 346 0 0 25.587302 34.05291 347 0 0 26.12963 34.771605 348 0 0 27.276596 34.673759 349 0 0 28.619048 36.071429 350 0 0 25 33.078947 351 0 0 23.909091 33 352 0 0 28.3 36.222222 353 0 0 25.782609 33.391304 354 0 0 25.3 32.783333 355 0 0 28.95 35.95 356 0 0 25.470588 34.823529 357 0 0 29.266667 36.555556 358 0 0 32.181818 38.727273 359 0 0 28.6 35.3 360 0 0 32.222222 38.62963 361 0 0 29.125 36.291667 362 0 0 23 30.444444 363 0 0 25.666667 35.055556 364 0 0 28.75 35.5 365 0 0 26.5 32 366 0 0 34.25 40 367 0 0 22.5 31.333333 368 0 0 36 41 369 0 0 36 41 370 0 0 36 41 371 0 0 4 9.333333 372 0 0 29 37