## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5376-Z0051-CACTTGCAGATCGAT/441525-L5376-Z0051-CACTTGCAGATCGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5376-Z0051-CACTTGCAGATCGAT/441525-L5376-Z0051-CACTTGCAGATCGAT_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 02:56:37 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 999226 999226 126 126716372 126716372 122012750 122012750 112717653 112717653 0 0 0.962881 0.889527 0 0.962881 0.889527 0 380149116 380149116 373905436 373905436 359280949 359280949 334335867 334335867 0.983576 0.945105 0.879486 0.983576 0.945105 0.879486 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 928 0 35.993045 40.994834 1 11366 0 35.986328 40.990614 2 14334 4327 35.993983 40.994939 3 35383 1249 35.977796 40.98257 4 56102 47865 35.99051 40.992298 5 110692 15371 35.994793 40.995683 6 113702 126542 35.941476 40.94796 7 194457 158123 35.964379 40.974218 8 201438 151960 35.992022 40.993648 9 238547 108023 35.958607 40.964354 10 248378 527175 35.824573 40.87826 11 286713 61019 35.937441 40.955575 12 323073 713533 35.206712 40.331799 13 334052 200299 33.582576 39.509699 14 426716 955135 35.868839 40.918321 15 368065 342140 35.805005 40.868085 16 360209 437606 35.808338 40.833954 17 495781 1026472 35.891693 40.910846 18 508715 692117 35.478372 40.560736 19 374971 674724 35.47768 40.592088 20 494359 969394 35.833382 40.887815 21 628996 1318610 35.769955 40.837418 22 323644 526857 35.48237 40.65289 23 1033886 1239736 35.170251 40.433585 24 557057 1142557 35.211064 40.466893 25 550416 463375 35.231498 40.480806 26 1797221 2479629 35.164196 40.427375 27 345880 884752 35.192743 40.453836 28 1003024 387197 35.213574 40.468041 29 2560614 5212380 35.207537 40.463068 30 809572 40003 35.212061 40.465063 31 2418402 842181 35.209365 40.462339 32 1632322 5591033 35.20806 40.456941 33 874859 122440 35.209667 40.46094 34 2526219 2741310 35.203855 40.458454 35 2219193 3850534 35.217942 40.468161 36 102237086 2127467 35.241518 40.483779 37 0 4233265 35.242744 40.486844 38 0 362637 35.231767 40.480311 39 0 5034212 35.228411 40.476627 40 0 1 35.223348 40.471296 41 0 334335866 35.214739 40.465841 42 0 0 35.208526 40.460818 43 0 0 35.213713 40.464703 44 0 0 35.224676 40.473402 45 0 0 35.22126 40.471306 46 0 0 35.209485 40.461543 47 0 0 35.195808 40.452628 48 0 0 35.171281 40.435139 49 0 0 35.173876 40.437597 50 0 0 35.166224 40.432607 51 0 0 35.152299 40.42477 52 0 0 35.13779 40.413537 53 0 0 35.116518 40.401407 54 0 0 35.106049 40.390974 55 0 0 35.084444 40.376343 56 0 0 35.035674 40.346576 57 0 0 35.022564 40.328848 58 0 0 34.985415 40.301637 59 0 0 34.935871 40.261848 60 0 0 34.879083 40.219806 61 0 0 34.795315 40.156241 62 0 0 34.717093 40.093158 63 0 0 34.634582 40.031529 64 0 0 34.549491 39.964924 65 0 0 34.454355 39.892607 66 0 0 34.352874 39.818 67 0 0 34.234127 39.727244 68 0 0 34.12455 39.643269 69 0 0 34.001522 39.54796 70 0 0 33.867772 39.438205 71 0 0 33.755211 39.349005 72 0 0 33.63644 39.250241 73 0 0 33.521335 39.154103 74 0 0 33.410085 39.068192 75 0 0 33.316393 38.992268 76 0 0 33.242539 38.932821 77 0 0 33.173227 38.883891 78 0 0 33.10005 38.825762 79 0 0 33.04721 38.782319 80 0 0 32.998717 38.738287 81 0 0 32.975295 38.713022 82 0 0 32.940892 38.682741 83 0 0 32.935764 38.675828 84 0 0 32.924595 38.663951 85 0 0 32.912212 38.651714 86 0 0 32.890474 38.629423 87 0 0 32.8617 38.607538 88 0 0 32.842112 38.588263 89 0 0 32.799612 38.549388 90 0 0 32.773508 38.523859 91 0 0 32.733361 38.486835 92 0 0 32.708608 38.462744 93 0 0 32.681289 38.437871 94 0 0 32.647488 38.410832 95 0 0 32.627608 38.395965 96 0 0 32.624776 38.393944 97 0 0 32.609725 38.379914 98 0 0 32.621774 38.392682 99 0 0 32.646309 38.410188 100 0 0 32.673516 38.429106 101 0 0 32.733636 38.477845 102 0 0 32.771222 38.508091 103 0 0 32.800315 38.52911 104 0 0 32.838354 38.557262 105 0 0 32.870792 38.579565 106 0 0 32.860951 38.570957 107 0 0 32.862385 38.569552 108 0 0 32.860804 38.571063 109 0 0 32.843073 38.555503 110 0 0 32.810395 38.531359 111 0 0 32.779612 38.506199 112 0 0 32.738682 38.472816 113 0 0 32.690911 38.432438 114 0 0 32.641302 38.393969 115 0 0 32.598345 38.356699 116 0 0 32.549671 38.324327 117 0 0 32.526092 38.311669 118 0 0 32.515404 38.301664 119 0 0 32.525037 38.313052 120 0 0 32.526426 38.315313 121 0 0 32.519026 38.306167 122 0 0 32.500441 38.292801 123 0 0 32.519187 38.305716 124 0 0 32.524846 38.308862 125 0 0 32.526623 38.310371 126 0 0 32.536214 38.320902 127 0 0 32.530125 38.312684 128 0 0 32.515328 38.294651 129 0 0 32.47496 38.260805 130 0 0 32.455108 38.241438 131 0 0 32.417902 38.208599 132 0 0 32.413314 38.20626 133 0 0 32.410531 38.20498 134 0 0 32.421914 38.212567 135 0 0 32.42191 38.206232 136 0 0 32.428535 38.212952 137 0 0 32.410726 38.196329 138 0 0 32.429061 38.215772 139 0 0 32.437183 38.219629 140 0 0 32.449662 38.231629 141 0 0 32.506064 38.280778 142 0 0 32.524348 38.292024 143 0 0 32.524268 38.284623 144 0 0 32.521568 38.282368 145 0 0 32.518762 38.279493 146 0 0 32.488927 38.253019 147 0 0 32.464707 38.23043 148 0 0 32.448649 38.214215 149 0 0 32.405547 38.185285 150 0 0 32.388305 38.172321 151 0 0 32.370631 38.150751 152 0 0 32.347218 38.136896 153 0 0 32.320471 38.111403 154 0 0 32.339265 38.128878 155 0 0 32.33025 38.121027 156 0 0 32.310378 38.106705 157 0 0 32.32034 38.118196 158 0 0 32.386818 38.168423 159 0 0 32.412175 38.190765 160 0 0 32.428307 38.199163 161 0 0 32.47296 38.238254 162 0 0 32.457796 38.229084 163 0 0 32.500365 38.260606 164 0 0 32.518351 38.274747 165 0 0 32.526073 38.280048 166 0 0 32.543695 38.292942 167 0 0 32.507736 38.260886 168 0 0 32.48398 38.241904 169 0 0 32.454672 38.212687 170 0 0 32.418202 38.182547 171 0 0 32.405531 38.170144 172 0 0 32.420031 38.181627 173 0 0 32.418002 38.189388 174 0 0 32.447525 38.213094 175 0 0 32.455105 38.218849 176 0 0 32.485767 38.252617 177 0 0 32.507074 38.2798 178 0 0 32.552401 38.3121 179 0 0 32.62285 38.369121 180 0 0 32.633852 38.376781 181 0 0 32.6674 38.408041 182 0 0 32.704495 38.441092 183 0 0 32.763713 38.476766 184 0 0 32.753724 38.47998 185 0 0 32.780916 38.49774 186 0 0 32.826838 38.536336 187 0 0 32.854057 38.56326 188 0 0 32.869977 38.575941 189 0 0 32.853254 38.570626 190 0 0 32.800884 38.525364 191 0 0 32.778564 38.511664 192 0 0 32.777937 38.518825 193 0 0 32.764463 38.505856 194 0 0 32.743639 38.505259 195 0 0 32.713375 38.483528 196 0 0 32.724216 38.492853 197 0 0 32.740029 38.521339 198 0 0 32.715636 38.506607 199 0 0 32.710686 38.503353 200 0 0 32.685469 38.497973 201 0 0 32.66807 38.492401 202 0 0 32.615913 38.455218 203 0 0 32.582678 38.42793 204 0 0 32.577963 38.442335 205 0 0 32.561244 38.431515 206 0 0 32.528727 38.400545 207 0 0 32.51086 38.392007 208 0 0 32.5703 38.44141 209 0 0 32.503969 38.39366 210 0 0 32.53104 38.424279 211 0 0 32.469364 38.393925 212 0 0 32.49875 38.40389 213 0 0 32.479068 38.403495 214 0 0 32.395404 38.340601 215 0 0 32.35931 38.308836 216 0 0 32.351425 38.312129 217 0 0 32.322785 38.302673 218 0 0 32.286143 38.289201 219 0 0 32.302841 38.294325 220 0 0 32.227518 38.232072 221 0 0 32.277805 38.272305 222 0 0 32.229552 38.234347 223 0 0 32.180366 38.203488 224 0 0 32.206104 38.227064 225 0 0 32.041868 38.103041 226 0 0 32.07298 38.134564 227 0 0 32.088107 38.133001 228 0 0 32.011326 38.102748 229 0 0 32.053299 38.130666 230 0 0 31.992356 38.079684 231 0 0 31.968668 38.063087 232 0 0 31.903384 38.012321 233 0 0 31.972346 38.076291 234 0 0 31.864124 38.01226 235 0 0 31.882001 38.036867 236 0 0 31.775133 37.936347 237 0 0 31.761982 37.926783 238 0 0 31.741865 37.924437 239 0 0 31.657531 37.861691 240 0 0 31.686811 37.883171 241 0 0 31.683613 37.910246 242 0 0 31.540208 37.766241 243 0 0 31.787868 37.967704 244 0 0 31.640203 37.889537 245 0 0 31.271423 37.595586 246 0 0 31.431603 37.708613 247 0 0 31.295393 37.606331 248 0 0 31.195723 37.548427 249 0 0 31.214143 37.633124 250 0 0 31.248883 37.642629 251 0 0 31.068629 37.46304 252 0 0 31.193974 37.584204 253 0 0 31.183428 37.585458 254 0 0 31.0381 37.502792 255 0 0 31.018501 37.479051 256 0 0 31.01996 37.428524 257 0 0 31.157043 37.554873 258 0 0 31.116836 37.545802 259 0 0 30.909529 37.387806 260 0 0 30.818614 37.281929 261 0 0 30.758516 37.296002 262 0 0 30.843388 37.360682 263 0 0 30.739195 37.299884 264 0 0 30.679826 37.270614 265 0 0 30.620553 37.257356 266 0 0 30.701754 37.262618 267 0 0 30.540947 37.143825 268 0 0 30.35835 37.010885 269 0 0 30.553129 37.162436 270 0 0 30.207243 36.896125 271 0 0 30.29125 37.0075 272 0 0 30.495345 37.163831 273 0 0 30.269218 36.982844 274 0 0 30.09094 36.919619 275 0 0 30.122936 36.891816 276 0 0 30.032876 36.829359 277 0 0 29.929049 36.805102 278 0 0 29.680518 36.617486 279 0 0 29.510989 36.498299 280 0 0 29.525314 36.5538 281 0 0 29.466778 36.513303 282 0 0 28.893672 36.122256 283 0 0 29.222272 36.263846 284 0 0 28.961486 36.170564 285 0 0 28.639618 35.898966 286 0 0 29.325444 36.47551 287 0 0 28.669046 35.862995 288 0 0 29.108079 36.190476 289 0 0 28.816246 36.046872 290 0 0 29.078261 36.23401 291 0 0 28.803767 36.081814 292 0 0 28.423344 35.754364 293 0 0 28.857236 35.994324 294 0 0 28.662799 35.933561 295 0 0 29.043634 36.200286 296 0 0 28.5994 35.782446 297 0 0 28.695343 35.895291 298 0 0 28.884519 36.122176 299 0 0 28.610868 35.992404 300 0 0 28.714676 36.050137 301 0 0 28.230916 35.677163 302 0 0 28.148703 35.562542 303 0 0 28.535714 35.762255 304 0 0 28.126096 35.644371 305 0 0 28.093458 35.54595 306 0 0 28.446363 35.748459 307 0 0 28.464146 35.814863 308 0 0 27.95 35.24537 309 0 0 28.734027 35.930163 310 0 0 27.985413 35.54241 311 0 0 27.757732 35.382016 312 0 0 27.572222 35.185185 313 0 0 28.346614 35.77158 314 0 0 28.030172 35.406609 315 0 0 27.897912 35.552978 316 0 0 28.640306 36.055272 317 0 0 27.804533 35.285175 318 0 0 28.178683 35.687565 319 0 0 28.363014 35.571918 320 0 0 27.286792 34.850314 321 0 0 27.029167 34.801389 322 0 0 27.679245 35.174528 323 0 0 28.125 35.074653 324 0 0 26.820359 34.469062 325 0 0 27.610738 35.322148 326 0 0 28.711111 35.869136 327 0 0 27.846774 35.341398 328 0 0 28.884956 36.20354 329 0 0 28.190476 35.511111 330 0 0 24.02 32.626667 331 0 0 27.068966 34.846743 332 0 0 28.02439 35.552846 333 0 0 26.216216 34.481982 334 0 0 26.215385 33.989744 335 0 0 27.403226 35.268817 336 0 0 26.8 34.145455 337 0 0 29.5 36.263889 338 0 0 26.071429 34.52381 339 0 0 27.368421 35.491228 340 0 0 23.685714 32.12381 341 0 0 28.709677 36.16129 342 0 0 26.892857 35.095238 343 0 0 30.461538 36.923077 344 0 0 30.333333 36.936508 345 0 0 29.055556 36.481481 346 0 0 23.941176 33.254902 347 0 0 27 34.871795 348 0 0 27.818182 36 349 0 0 33.555556 39.259259 350 0 0 25.25 35.041667 351 0 0 25.714286 33.190476 352 0 0 28.666667 36.722222 353 0 0 25.166667 33.944444 354 0 0 32.833333 38.277778 355 0 0 25.833333 32.277778 356 0 0 23.5 32.75 357 0 0 34.5 39.916667 358 0 0 32.75 38.333333 359 0 0 27.333333 37.555556 360 0 0 33.5 39.5 361 0 0 32 37.666667 362 0 0 26 36 363 0 0 6 11.333333 364 0 0 7 12 365 0 0 23 31 366 0 0 23 35 367 0 0 36 41 368 0 0 23 35