## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5280-Z0023-CATGGAGATACTGAT/441525-L5280-Z0023-CATGGAGATACTGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5280-Z0023-CATGGAGATACTGAT/441525-L5280-Z0023-CATGGAGATACTGAT_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 02:54:45 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 997268 997268 180 180177944 180177944 175404676 175404676 165677492 165677492 0 0 0.973508 0.919521 0 0.973508 0.919521 0 540533832 540533832 534375103 534375103 519118842 519118842 492618596 492618596 0.988606 0.960382 0.911356 0.988606 0.960382 0.911356 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 1096 0 35.992414 40.994412 1 14988 1 35.987262 40.99151 2 17831 7073 35.992615 40.993618 3 43033 1821 35.980199 40.983829 4 61409 60457 35.988366 40.990551 5 128228 17027 35.993994 40.995024 6 96993 155945 35.969921 40.976278 7 210346 180325 35.979371 40.985607 8 168905 150347 35.987964 40.99019 9 241117 118752 35.931646 40.942438 10 250661 492593 35.908196 40.936464 11 292934 71518 35.950293 40.964845 12 334724 685464 35.595959 40.661728 13 319019 196967 34.725109 40.212212 14 454274 927007 35.907825 40.945648 15 374468 380133 35.737667 40.822046 16 348507 366369 35.762548 40.792136 17 500176 990278 35.913066 40.928824 18 539171 721317 35.693442 40.75704 19 375388 635335 35.814477 40.866959 20 585539 920655 35.942388 40.96088 21 676011 1387057 35.844897 40.888371 22 369071 510662 35.641685 40.759582 23 1244731 1497598 35.397924 40.595809 24 608400 1244938 35.436746 40.616205 25 541358 509909 35.420014 40.606164 26 1882196 2693289 35.37674 40.57545 27 374588 984877 35.40103 40.597096 28 944510 437784 35.404573 40.598743 29 2500780 5069492 35.394912 40.59154 30 845154 54725 35.396611 40.590854 31 2547768 1085129 35.395992 40.590977 32 1924637 5232405 35.392111 40.586197 33 966709 161600 35.388587 40.585609 34 2736684 3230842 35.380953 40.581417 35 2540138 3736602 35.396208 40.591378 36 154116402 2742311 35.412236 40.602215 37 0 4243038 35.414929 40.605013 38 0 594089 35.404037 40.599165 39 0 5419505 35.404461 40.597664 40 0 1 35.396039 40.591627 41 0 492618595 35.382151 40.581632 42 0 0 35.370025 40.573512 43 0 0 35.371505 40.574965 44 0 0 35.383325 40.582749 45 0 0 35.383632 40.58171 46 0 0 35.38085 40.581095 47 0 0 35.376274 40.577935 48 0 0 35.368984 40.57351 49 0 0 35.363282 40.56901 50 0 0 35.361633 40.566797 51 0 0 35.362467 40.567039 52 0 0 35.348931 40.558679 53 0 0 35.342618 40.554973 54 0 0 35.343392 40.555587 55 0 0 35.332998 40.548857 56 0 0 35.323311 40.543265 57 0 0 35.320488 40.538254 58 0 0 35.316674 40.534653 59 0 0 35.299904 40.523104 60 0 0 35.290066 40.515077 61 0 0 35.287257 40.510317 62 0 0 35.257835 40.489017 63 0 0 35.230201 40.469635 64 0 0 35.2134 40.455703 65 0 0 35.193927 40.442278 66 0 0 35.164782 40.42156 67 0 0 35.145027 40.403772 68 0 0 35.113093 40.382969 69 0 0 35.079526 40.356882 70 0 0 35.047457 40.331039 71 0 0 35.027819 40.313876 72 0 0 34.981513 40.278569 73 0 0 34.952065 40.254234 74 0 0 34.916709 40.227183 75 0 0 34.884387 40.201272 76 0 0 34.83917 40.165428 77 0 0 34.805642 40.140294 78 0 0 34.771257 40.114259 79 0 0 34.736347 40.087769 80 0 0 34.702514 40.059366 81 0 0 34.666774 40.030064 82 0 0 34.62801 39.999293 83 0 0 34.611035 39.984817 84 0 0 34.591109 39.967799 85 0 0 34.561335 39.944599 86 0 0 34.544972 39.930924 87 0 0 34.531162 39.921783 88 0 0 34.510759 39.900829 89 0 0 34.485656 39.883175 90 0 0 34.473906 39.87228 91 0 0 34.454055 39.854699 92 0 0 34.442921 39.84405 93 0 0 34.437104 39.837001 94 0 0 34.419242 39.821561 95 0 0 34.405187 39.810633 96 0 0 34.404392 39.809025 97 0 0 34.389316 39.795992 98 0 0 34.382183 39.791372 99 0 0 34.387161 39.793625 100 0 0 34.380564 39.788283 101 0 0 34.383855 39.790668 102 0 0 34.396672 39.799712 103 0 0 34.403564 39.802346 104 0 0 34.413264 39.811556 105 0 0 34.421055 39.814861 106 0 0 34.427827 39.818761 107 0 0 34.433862 39.825546 108 0 0 34.43829 39.828578 109 0 0 34.447089 39.835457 110 0 0 34.442074 39.832753 111 0 0 34.43532 39.825848 112 0 0 34.418024 39.811022 113 0 0 34.400648 39.795179 114 0 0 34.384275 39.780516 115 0 0 34.367537 39.764734 116 0 0 34.349244 39.754215 117 0 0 34.336412 39.74593 118 0 0 34.337378 39.746933 119 0 0 34.332704 39.742158 120 0 0 34.327946 39.741693 121 0 0 34.327935 39.739999 122 0 0 34.32444 39.735557 123 0 0 34.316623 39.728914 124 0 0 34.3233 39.73283 125 0 0 34.327705 39.734357 126 0 0 34.340322 39.745339 127 0 0 34.345892 39.74698 128 0 0 34.358428 39.756026 129 0 0 34.358323 39.758126 130 0 0 34.353964 39.752992 131 0 0 34.361474 39.759196 132 0 0 34.355996 39.755432 133 0 0 34.351317 39.748769 134 0 0 34.356144 39.752085 135 0 0 34.353314 39.747108 136 0 0 34.338299 39.734375 137 0 0 34.336326 39.733506 138 0 0 34.325817 39.725786 139 0 0 34.328557 39.730024 140 0 0 34.340248 39.740479 141 0 0 34.349146 39.749123 142 0 0 34.36031 39.75695 143 0 0 34.360679 39.756546 144 0 0 34.344475 39.743482 145 0 0 34.343313 39.741629 146 0 0 34.331555 39.72869 147 0 0 34.322595 39.720012 148 0 0 34.306796 39.710002 149 0 0 34.283859 39.692081 150 0 0 34.265604 39.674701 151 0 0 34.251072 39.664508 152 0 0 34.22835 39.648428 153 0 0 34.216941 39.641214 154 0 0 34.212726 39.632899 155 0 0 34.186795 39.612761 156 0 0 34.175213 39.602087 157 0 0 34.152252 39.581914 158 0 0 34.153651 39.584023 159 0 0 34.152257 39.581369 160 0 0 34.145785 39.576756 161 0 0 34.150946 39.581545 162 0 0 34.151538 39.581131 163 0 0 34.139806 39.5735 164 0 0 34.144079 39.575457 165 0 0 34.123228 39.55766 166 0 0 34.098863 39.537078 167 0 0 34.062401 39.50403 168 0 0 34.024304 39.470642 169 0 0 33.960776 39.419129 170 0 0 33.902913 39.371298 171 0 0 33.854266 39.326851 172 0 0 33.800272 39.283386 173 0 0 33.76396 39.254039 174 0 0 33.714319 39.21412 175 0 0 33.70024 39.20296 176 0 0 33.658876 39.165396 177 0 0 33.646968 39.155319 178 0 0 33.620808 39.133254 179 0 0 33.612667 39.126457 180 0 0 33.614989 39.127288 181 0 0 33.597767 39.114177 182 0 0 33.605802 39.121476 183 0 0 33.611009 39.126776 184 0 0 33.636116 39.146034 185 0 0 33.647919 39.153789 186 0 0 33.662576 39.165411 187 0 0 33.679118 39.18052 188 0 0 33.692341 39.192468 189 0 0 33.693181 39.189666 190 0 0 33.703852 39.197553 191 0 0 33.696779 39.192375 192 0 0 33.679537 39.179497 193 0 0 33.668678 39.177889 194 0 0 33.655805 39.169053 195 0 0 33.650574 39.168074 196 0 0 33.632203 39.157499 197 0 0 33.618854 39.149753 198 0 0 33.604275 39.143674 199 0 0 33.582269 39.132453 200 0 0 33.560517 39.119376 201 0 0 33.535226 39.105338 202 0 0 33.500667 39.091368 203 0 0 33.475898 39.07332 204 0 0 33.436251 39.047001 205 0 0 33.411993 39.037366 206 0 0 33.377474 39.020776 207 0 0 33.352426 39.004659 208 0 0 33.313581 38.982196 209 0 0 33.288513 38.969547 210 0 0 33.272669 38.963488 211 0 0 33.230806 38.938894 212 0 0 33.180404 38.909951 213 0 0 33.143621 38.882521 214 0 0 33.109612 38.864455 215 0 0 33.061205 38.834101 216 0 0 33.029933 38.814312 217 0 0 33.026089 38.813464 218 0 0 32.990279 38.789814 219 0 0 32.966594 38.777977 220 0 0 32.9123 38.737226 221 0 0 32.897836 38.737293 222 0 0 32.868429 38.714414 223 0 0 32.858805 38.709856 224 0 0 32.81517 38.678602 225 0 0 32.783098 38.660074 226 0 0 32.757808 38.642783 227 0 0 32.727219 38.621628 228 0 0 32.685839 38.598869 229 0 0 32.691075 38.601555 230 0 0 32.640833 38.568019 231 0 0 32.634084 38.567879 232 0 0 32.600125 38.543192 233 0 0 32.57417 38.523626 234 0 0 32.512237 38.495095 235 0 0 32.525802 38.496289 236 0 0 32.466504 38.455626 237 0 0 32.433476 38.441689 238 0 0 32.376352 38.397732 239 0 0 32.385087 38.41333 240 0 0 32.357959 38.39286 241 0 0 32.314902 38.366124 242 0 0 32.301542 38.35841 243 0 0 32.264903 38.334411 244 0 0 32.250846 38.328086 245 0 0 32.179025 38.275515 246 0 0 32.125849 38.250194 247 0 0 32.119894 38.24071 248 0 0 32.081826 38.220385 249 0 0 32.068215 38.213201 250 0 0 32.068064 38.207356 251 0 0 32.021139 38.182286 252 0 0 31.992275 38.171621 253 0 0 31.945969 38.140267 254 0 0 31.862712 38.086855 255 0 0 31.874718 38.097799 256 0 0 31.795523 38.041231 257 0 0 31.780684 38.039763 258 0 0 31.74008 38.016175 259 0 0 31.694193 37.978853 260 0 0 31.634175 37.946743 261 0 0 31.62954 37.940648 262 0 0 31.585249 37.915513 263 0 0 31.514151 37.869092 264 0 0 31.496406 37.861412 265 0 0 31.48354 37.857575 266 0 0 31.367139 37.770546 267 0 0 31.370209 37.775963 268 0 0 31.261042 37.705548 269 0 0 31.237696 37.672649 270 0 0 31.15137 37.62179 271 0 0 31.102283 37.599294 272 0 0 31.050371 37.56067 273 0 0 31.049992 37.562113 274 0 0 30.940591 37.489497 275 0 0 30.880359 37.455612 276 0 0 30.786624 37.384196 277 0 0 30.755464 37.367374 278 0 0 30.682744 37.323542 279 0 0 30.539769 37.214219 280 0 0 30.620551 37.278899 281 0 0 30.446535 37.148428 282 0 0 30.417675 37.146736 283 0 0 30.329778 37.07695 284 0 0 30.262196 37.032928 285 0 0 30.287488 37.040703 286 0 0 30.182915 36.986095 287 0 0 30.073857 36.902233 288 0 0 30.072961 36.918923 289 0 0 30.044211 36.891421 290 0 0 29.946961 36.832501 291 0 0 29.895064 36.764619 292 0 0 29.86049 36.754631 293 0 0 29.778233 36.695852 294 0 0 29.756894 36.678136 295 0 0 29.524415 36.514979 296 0 0 29.630591 36.608378 297 0 0 29.581369 36.538428 298 0 0 29.448036 36.461799 299 0 0 29.523388 36.520029 300 0 0 29.399529 36.416217 301 0 0 29.401792 36.441022 302 0 0 29.336346 36.374124 303 0 0 29.308325 36.347853 304 0 0 29.140149 36.25416 305 0 0 29.190688 36.264703 306 0 0 29.175516 36.296325 307 0 0 29.020945 36.166214 308 0 0 28.988194 36.129573 309 0 0 28.986706 36.120901 310 0 0 28.975782 36.126784 311 0 0 28.888897 36.064283 312 0 0 28.840151 36.058545 313 0 0 28.837669 36.01447 314 0 0 28.773449 35.960162 315 0 0 28.804255 35.993302 316 0 0 28.891443 36.057897 317 0 0 28.679241 35.941904 318 0 0 28.751535 35.96255 319 0 0 28.695888 35.922761 320 0 0 28.82041 36.023093 321 0 0 28.606078 35.865688 322 0 0 28.615605 35.79358 323 0 0 28.745176 35.975201 324 0 0 28.508923 35.831126 325 0 0 28.539987 35.820145 326 0 0 28.708747 35.931918 327 0 0 28.613052 35.920007 328 0 0 28.648301 35.860215 329 0 0 28.374726 35.725263 330 0 0 28.312873 35.62177 331 0 0 28.514331 35.744929 332 0 0 28.715091 35.917895 333 0 0 28.068699 35.488308 334 0 0 28.169437 35.578374 335 0 0 28.485196 35.781873 336 0 0 28.415353 35.751885 337 0 0 28.304485 35.618148 338 0 0 28.373239 35.727993 339 0 0 28.222672 35.622132 340 0 0 28.451945 35.774218 341 0 0 27.845752 35.401743 342 0 0 27.64645 35.177022 343 0 0 28.353448 35.654598 344 0 0 27.935547 35.229167 345 0 0 27.604706 35.09098 346 0 0 28.060052 35.430809 347 0 0 28.751497 36.181637 348 0 0 28.65371 35.971731 349 0 0 29.15102 36.27483 350 0 0 27.938967 35.521127 351 0 0 27.407821 34.875233 352 0 0 29.043478 36.215321 353 0 0 27.251748 34.874126 354 0 0 26.468254 34.029101 355 0 0 29.216981 36.509434 356 0 0 27.772727 34.92803 357 0 0 26.933333 34.626667 358 0 0 29.274194 36.258065 359 0 0 29.188679 36.610063 360 0 0 29.468085 36.992908 361 0 0 28.26087 35.73913 362 0 0 30 37.578947 363 0 0 26.575758 34.737374 364 0 0 30.931034 37.942529 365 0 0 30.592593 37.493827 366 0 0 25.458333 33.319444 367 0 0 29.863636 36.454545 368 0 0 26.8 35.366667 369 0 0 26.055556 34.37037 370 0 0 30.333333 37.577778 371 0 0 25.714286 33.452381 372 0 0 32.923077 39.102564 373 0 0 26.384615 35.230769 374 0 0 30.416667 37.222222 375 0 0 28.25 35.305556 376 0 0 28 35.305556 377 0 0 24.4 32.766667 378 0 0 25.777778 35.62963 379 0 0 31.75 38.166667 380 0 0 24.857143 33 381 0 0 30.428571 37.190476 382 0 0 27.571429 34.238095 383 0 0 33.5 39.083333 384 0 0 34.333333 39.777778 385 0 0 28 36.777778 386 0 0 36 41 387 0 0 35.333333 40.111111 388 0 0 31.666667 38.111111 389 0 0 26.666667 36.888889 390 0 0 29.333333 35.888889 391 0 0 36 41 392 0 0 31.5 38.166667 393 0 0 32.5 38.666667 394 0 0 34.5 40 395 0 0 28 37.5 396 0 0 36 41 397 0 0 5 24.333333 398 0 0 33 38.666667 399 0 0 7 29.666667