## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5387-Z0072-CTATCTCATAATGAT/441525-L5387-Z0072-CTATCTCATAATGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5387-Z0072-CTATCTCATAATGAT/441525-L5387-Z0072-CTATCTCATAATGAT_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 02:59:58 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 998311 998311 135 135196559 135196559 130531786 130531786 121462147 121462147 0 0 0.965496 0.898412 0 0.965496 0.898412 0 405589677 405589677 399406869 399406869 385022919 385022919 360596193 360596193 0.984756 0.949292 0.889066 0.984756 0.949292 0.889066 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 701 0 35.99529 40.996395 1 9690 0 35.989262 40.992524 2 11906 3835 35.994554 40.995338 3 30216 1047 35.984035 40.986981 4 51904 40953 35.992947 40.994218 5 99423 14627 35.996727 40.997265 6 111382 108204 35.972668 40.976914 7 178851 140318 35.980708 40.986532 8 188270 143649 35.992371 40.993814 9 223732 94381 35.961217 40.967723 10 231499 497123 35.906423 40.942882 11 276559 52915 35.932914 40.950197 12 329810 671247 35.258126 40.38135 13 341236 199546 33.909173 39.704523 14 433805 953412 35.888472 40.931168 15 353663 346068 35.84183 40.887911 16 375282 438902 35.791454 40.815785 17 509832 1096605 35.892993 40.908798 18 535353 679347 35.712092 40.763058 19 371659 700629 35.729649 40.795009 20 488185 1006113 35.909537 40.939313 21 634971 1315941 35.860684 40.89967 22 315530 559756 35.65237 40.764317 23 1006827 1153235 35.400323 40.592298 24 559450 1137164 35.4015 40.594658 25 541751 472842 35.413516 40.604464 26 1757028 2488626 35.3567 40.560805 27 344852 855066 35.365324 40.570037 28 956601 360678 35.394666 40.590859 29 2464444 5034529 35.391232 40.586473 30 749331 39422 35.386494 40.582454 31 2316524 781338 35.37629 40.573999 32 1555404 5428045 35.373638 40.570286 33 829205 117821 35.375676 40.573437 34 2436156 2508829 35.366008 40.566682 35 2225343 3874547 35.381453 40.577722 36 111350184 1967641 35.39617 40.588229 37 0 4313038 35.398175 40.59046 38 0 372303 35.39686 40.589523 39 0 5023742 35.389561 40.584758 40 0 1 35.383219 40.578574 41 0 360596192 35.376248 40.57353 42 0 0 35.374214 40.573243 43 0 0 35.373396 40.571747 44 0 0 35.377687 40.575191 45 0 0 35.387651 40.582241 46 0 0 35.382164 40.577167 47 0 0 35.372706 40.570748 48 0 0 35.364935 40.566332 49 0 0 35.364937 40.565446 50 0 0 35.364206 40.5655 51 0 0 35.354296 40.558128 52 0 0 35.337992 40.548068 53 0 0 35.336338 40.548476 54 0 0 35.32851 40.542775 55 0 0 35.319712 40.535423 56 0 0 35.30978 40.529422 57 0 0 35.299705 40.520669 58 0 0 35.288228 40.512377 59 0 0 35.258346 40.490419 60 0 0 35.238153 40.474708 61 0 0 35.206467 40.451669 62 0 0 35.164544 40.42086 63 0 0 35.128757 40.394698 64 0 0 35.084336 40.361249 65 0 0 35.03547 40.325128 66 0 0 34.979778 40.283132 67 0 0 34.913422 40.235147 68 0 0 34.840805 40.180619 69 0 0 34.752618 40.114576 70 0 0 34.662626 40.044 71 0 0 34.561312 39.965754 72 0 0 34.458802 39.882691 73 0 0 34.351321 39.797641 74 0 0 34.242045 39.711137 75 0 0 34.142503 39.634271 76 0 0 34.041215 39.553852 77 0 0 33.931721 39.471012 78 0 0 33.838747 39.403235 79 0 0 33.747004 39.327758 80 0 0 33.677116 39.27197 81 0 0 33.598978 39.210352 82 0 0 33.521365 39.14701 83 0 0 33.463844 39.101525 84 0 0 33.414748 39.060511 85 0 0 33.363771 39.019557 86 0 0 33.30522 38.970409 87 0 0 33.265719 38.937921 88 0 0 33.213117 38.89257 89 0 0 33.167342 38.853585 90 0 0 33.097851 38.795764 91 0 0 33.047225 38.750948 92 0 0 33.016669 38.725204 93 0 0 32.967935 38.68406 94 0 0 32.939501 38.656672 95 0 0 32.915799 38.635991 96 0 0 32.886889 38.611811 97 0 0 32.869798 38.596397 98 0 0 32.868458 38.596954 99 0 0 32.8826 38.605691 100 0 0 32.929374 38.640857 101 0 0 32.955272 38.662892 102 0 0 32.989625 38.690093 103 0 0 33.036662 38.725149 104 0 0 33.050775 38.733152 105 0 0 33.07204 38.746265 106 0 0 33.072549 38.743944 107 0 0 33.061989 38.731871 108 0 0 33.053105 38.720388 109 0 0 33.021826 38.702793 110 0 0 32.984976 38.671903 111 0 0 32.943206 38.638237 112 0 0 32.881985 38.59048 113 0 0 32.826039 38.544599 114 0 0 32.769413 38.499298 115 0 0 32.706545 38.447866 116 0 0 32.657773 38.409844 117 0 0 32.640142 38.398832 118 0 0 32.635726 38.396941 119 0 0 32.636812 38.399439 120 0 0 32.638088 38.400274 121 0 0 32.657955 38.415981 122 0 0 32.651422 38.410069 123 0 0 32.667429 38.419572 124 0 0 32.685098 38.429788 125 0 0 32.693676 38.434317 126 0 0 32.704928 38.434762 127 0 0 32.711324 38.440669 128 0 0 32.688821 38.415768 129 0 0 32.658006 38.388349 130 0 0 32.619302 38.354353 131 0 0 32.594483 38.336434 132 0 0 32.580061 38.327442 133 0 0 32.560348 38.309647 134 0 0 32.556854 38.304446 135 0 0 32.552851 38.299612 136 0 0 32.539301 38.28471 137 0 0 32.538256 38.286459 138 0 0 32.526109 38.277073 139 0 0 32.557915 38.302729 140 0 0 32.570155 38.316295 141 0 0 32.603608 38.342382 142 0 0 32.61616 38.354252 143 0 0 32.60921 38.344433 144 0 0 32.604132 38.34251 145 0 0 32.606234 38.336029 146 0 0 32.550053 38.285838 147 0 0 32.523186 38.264022 148 0 0 32.492109 38.242004 149 0 0 32.45479 38.20374 150 0 0 32.426156 38.187704 151 0 0 32.389564 38.153904 152 0 0 32.352325 38.125949 153 0 0 32.363498 38.138711 154 0 0 32.355734 38.133867 155 0 0 32.344361 38.117773 156 0 0 32.376857 38.149427 157 0 0 32.419112 38.180581 158 0 0 32.442709 38.19367 159 0 0 32.490152 38.235742 160 0 0 32.51231 38.251567 161 0 0 32.523003 38.257643 162 0 0 32.590948 38.315533 163 0 0 32.59886 38.324858 164 0 0 32.621742 38.338143 165 0 0 32.65655 38.361808 166 0 0 32.639993 38.345584 167 0 0 32.613024 38.320023 168 0 0 32.595338 38.301688 169 0 0 32.543975 38.255914 170 0 0 32.515871 38.237716 171 0 0 32.492691 38.218586 172 0 0 32.488857 38.215876 173 0 0 32.528916 38.248838 174 0 0 32.553578 38.271341 175 0 0 32.551445 38.273953 176 0 0 32.57072 38.29242 177 0 0 32.612414 38.329924 178 0 0 32.666269 38.376765 179 0 0 32.734727 38.426757 180 0 0 32.725226 38.424468 181 0 0 32.813473 38.494551 182 0 0 32.85863 38.529035 183 0 0 32.911981 38.576404 184 0 0 32.918961 38.585774 185 0 0 32.934803 38.601197 186 0 0 33.017078 38.66067 187 0 0 33.00085 38.648449 188 0 0 33.036684 38.674103 189 0 0 33.067749 38.707097 190 0 0 33.054356 38.694503 191 0 0 33.053774 38.702811 192 0 0 33.021662 38.683468 193 0 0 32.985458 38.657221 194 0 0 32.975831 38.654728 195 0 0 32.9873 38.673448 196 0 0 32.946115 38.645297 197 0 0 32.95762 38.658014 198 0 0 32.981292 38.680522 199 0 0 32.955739 38.671118 200 0 0 32.937661 38.656484 201 0 0 32.932613 38.6639 202 0 0 32.945877 38.676572 203 0 0 32.922604 38.674288 204 0 0 32.902939 38.6671 205 0 0 32.869497 38.652908 206 0 0 32.889948 38.68404 207 0 0 32.92053 38.691316 208 0 0 32.859331 38.659825 209 0 0 32.832727 38.640753 210 0 0 32.79623 38.615919 211 0 0 32.837973 38.644841 212 0 0 32.799814 38.625041 213 0 0 32.70493 38.567375 214 0 0 32.763807 38.59613 215 0 0 32.713234 38.561456 216 0 0 32.738198 38.582245 217 0 0 32.736146 38.593598 218 0 0 32.644428 38.528233 219 0 0 32.652944 38.530454 220 0 0 32.667693 38.552949 221 0 0 32.55097 38.464091 222 0 0 32.595651 38.491484 223 0 0 32.550144 38.47558 224 0 0 32.561996 38.488799 225 0 0 32.473595 38.426552 226 0 0 32.48412 38.435368 227 0 0 32.542769 38.470694 228 0 0 32.419031 38.405956 229 0 0 32.437755 38.401581 230 0 0 32.480625 38.439795 231 0 0 32.466193 38.433691 232 0 0 32.451952 38.425988 233 0 0 32.39197 38.384566 234 0 0 32.413314 38.397234 235 0 0 32.385008 38.394332 236 0 0 32.365322 38.390355 237 0 0 32.344182 38.366217 238 0 0 32.24063 38.284443 239 0 0 32.327327 38.384364 240 0 0 32.239045 38.283734 241 0 0 32.209974 38.289725 242 0 0 32.164197 38.248056 243 0 0 32.121023 38.201475 244 0 0 32.207014 38.271791 245 0 0 32.118599 38.207604 246 0 0 31.99698 38.14675 247 0 0 32.134029 38.228603 248 0 0 31.98664 38.113588 249 0 0 32.058225 38.184986 250 0 0 31.888672 38.066139 251 0 0 31.972871 38.137987 252 0 0 31.943234 38.100365 253 0 0 31.914219 38.106629 254 0 0 31.741502 38.001904 255 0 0 31.787926 38.025872 256 0 0 31.750403 37.969941 257 0 0 31.66553 37.913163 258 0 0 31.733503 37.984182 259 0 0 31.61516 37.900884 260 0 0 31.598668 37.892305 261 0 0 31.479982 37.816955 262 0 0 31.432041 37.803519 263 0 0 31.433517 37.800591 264 0 0 31.508439 37.841324 265 0 0 31.263356 37.71081 266 0 0 31.226626 37.648925 267 0 0 31.229941 37.649989 268 0 0 31.392963 37.739373 269 0 0 31.102426 37.582024 270 0 0 31.049365 37.55543 271 0 0 31.116597 37.587592 272 0 0 30.915696 37.480177 273 0 0 30.941894 37.493602 274 0 0 30.618478 37.287651 275 0 0 30.704684 37.321792 276 0 0 30.785634 37.346771 277 0 0 30.71452 37.288973 278 0 0 30.487821 37.141419 279 0 0 30.250722 36.997905 280 0 0 30.331595 37.080508 281 0 0 30.263899 37.023759 282 0 0 30.166027 36.96922 283 0 0 30.356313 37.061696 284 0 0 30.10287 36.904193 285 0 0 29.894383 36.783228 286 0 0 29.699144 36.628346 287 0 0 29.935294 36.778922 288 0 0 29.709615 36.691497 289 0 0 29.618547 36.610801 290 0 0 29.336479 36.412198 291 0 0 29.471415 36.480229 292 0 0 29.525953 36.543829 293 0 0 29.352822 36.422725 294 0 0 29.419916 36.410256 295 0 0 29.54493 36.514519 296 0 0 29.283637 36.361555 297 0 0 29.432649 36.413222 298 0 0 28.94396 36.119344 299 0 0 28.959177 36.104071 300 0 0 29.02059 36.181652 301 0 0 28.577658 35.84973 302 0 0 28.942183 36.080512 303 0 0 28.864168 36.068521 304 0 0 28.67422 35.984181 305 0 0 28.547306 35.857251 306 0 0 28.872931 36.040084 307 0 0 28.309166 35.650268 308 0 0 28.911863 36.161863 309 0 0 28.484902 35.875074 310 0 0 28.139417 35.555133 311 0 0 28.622873 35.843885 312 0 0 28.44797 35.788438 313 0 0 28.32856 35.698754 314 0 0 28.374573 35.612628 315 0 0 28.146274 35.493714 316 0 0 28.285572 35.584411 317 0 0 28.43194 35.792783 318 0 0 28.248837 35.573643 319 0 0 28.244025 35.650734 320 0 0 28.017833 35.472337 321 0 0 28.480655 35.72619 322 0 0 27.797078 35.147727 323 0 0 27.50991 35.02042 324 0 0 27.647295 35.262525 325 0 0 27.479121 35.081319 326 0 0 27.897059 35.485294 327 0 0 28.737705 35.717668 328 0 0 27.631579 35.226121 329 0 0 28.424749 35.822742 330 0 0 27.518797 35.06391 331 0 0 27.438525 34.972678 332 0 0 27.84375 35.104167 333 0 0 27.598985 35.118443 334 0 0 27.711765 35.184314 335 0 0 27.173333 34.877778 336 0 0 28.007463 35.624378 337 0 0 27.974359 35.655271 338 0 0 26.892157 34.650327 339 0 0 25.902174 34.188406 340 0 0 28.280488 35.878049 341 0 0 28.25 35.532407 342 0 0 27.78125 35.140625 343 0 0 27.056604 35.245283 344 0 0 25.897959 33.217687 345 0 0 26.108696 33.775362 346 0 0 26.536585 34.121951 347 0 0 27.4 35.809524 348 0 0 28.78125 36 349 0 0 26.071429 33.761905 350 0 0 24.296296 32.271605 351 0 0 28.458333 35.694444 352 0 0 25.117647 32.745098 353 0 0 23.2 32.555556 354 0 0 28.428571 35.571429 355 0 0 27.166667 36.055556 356 0 0 28 34.636364 357 0 0 27.1 34.1 358 0 0 24 31.571429 359 0 0 30.571429 36 360 0 0 28.333333 35.666667 361 0 0 30 36.388889 362 0 0 23.5 32 363 0 0 30.833333 37 364 0 0 31.166667 36.888889 365 0 0 31.5 37.222222 366 0 0 14 23.666667 367 0 0 23.75 35.333333 368 0 0 31 36.888889 369 0 0 30.666667 38.333333 370 0 0 20 29.5 371 0 0 21.5 30.333333 372 0 0 21 30.666667 373 0 0 12 31.333333