## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5404-Z0093-CAATGACAGCTCGAT/441525-L5404-Z0093-CAATGACAGCTCGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5404-Z0093-CAATGACAGCTCGAT/441525-L5404-Z0093-CAATGACAGCTCGAT_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 02:59:51 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 999786 999786 123 123448105 123448105 118613178 118613178 109588214 109588214 0 0 0.960834 0.887727 0 0.960834 0.887727 0 370344315 370344315 363901368 363901368 349454882 349454882 325432153 325432153 0.982603 0.943595 0.878729 0.982603 0.943595 0.878729 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 826 2 35.993473 40.994945 1 10248 0 35.984674 40.989181 2 12831 3837 35.994985 40.99573 3 31578 1022 35.982713 40.985904 4 52090 44361 35.988173 40.990406 5 104472 17368 35.991981 40.993206 6 110121 115368 35.973327 40.976983 7 186634 149649 35.976901 40.984269 8 195015 142578 35.987367 40.989939 9 232415 104406 35.959091 40.96544 10 246720 491088 35.893224 40.934645 11 294112 57125 35.931142 40.948868 12 354029 702018 35.154898 40.28601 13 355395 205673 33.453365 39.425037 14 456739 997315 35.886645 40.931116 15 366192 372831 35.837769 40.883884 16 392770 461305 35.803107 40.825313 17 515441 1132885 35.905099 40.920222 18 548337 724789 35.726872 40.774714 19 368962 719327 35.732298 40.800579 20 490044 1019214 35.902535 40.935372 21 653897 1344872 35.835491 40.88046 22 312175 569396 35.60269 40.72825 23 995822 1162024 35.286483 40.506342 24 568243 1154953 35.292788 40.518453 25 534640 468735 35.307535 40.530151 26 1720873 2476591 35.233429 40.473669 27 354195 834615 35.250502 40.490547 28 954730 367307 35.262524 40.499445 29 2440345 5048779 35.264761 40.49961 30 725354 37834 35.265112 40.499743 31 2296112 754041 35.260036 40.495298 32 1525083 5431836 35.249551 40.484547 33 797226 112607 35.254251 40.49104 34 2382045 2460254 35.249675 40.488228 35 2140507 3822850 35.266149 40.499288 36 99721887 1969191 35.291286 40.516576 37 0 4225923 35.287204 40.515 38 0 334996 35.280859 40.512458 39 0 4873197 35.28002 40.510551 40 0 0 35.275581 40.505348 41 0 325432153 35.261131 40.494743 42 0 0 35.258378 40.493581 43 0 0 35.267218 40.497306 44 0 0 35.265033 40.496777 45 0 0 35.276655 40.504637 46 0 0 35.269702 40.500135 47 0 0 35.260656 40.493748 48 0 0 35.245242 40.483668 49 0 0 35.23521 40.47681 50 0 0 35.230106 40.472271 51 0 0 35.220998 40.467086 52 0 0 35.195496 40.447173 53 0 0 35.168861 40.430566 54 0 0 35.158792 40.420556 55 0 0 35.127351 40.396054 56 0 0 35.092881 40.374363 57 0 0 35.080667 40.363943 58 0 0 35.033913 40.326823 59 0 0 34.976577 40.28563 60 0 0 34.919574 40.247745 61 0 0 34.854418 40.195776 62 0 0 34.778262 40.136196 63 0 0 34.696851 40.072686 64 0 0 34.606494 40.00323 65 0 0 34.505923 39.928684 66 0 0 34.394732 39.844835 67 0 0 34.279159 39.759334 68 0 0 34.151162 39.662723 69 0 0 34.007304 39.550801 70 0 0 33.857534 39.431111 71 0 0 33.70663 39.310132 72 0 0 33.550986 39.184605 73 0 0 33.402562 39.063443 74 0 0 33.256944 38.947748 75 0 0 33.119566 38.839349 76 0 0 32.992162 38.744401 77 0 0 32.884431 38.662048 78 0 0 32.781682 38.581692 79 0 0 32.686423 38.505643 80 0 0 32.621134 38.450679 81 0 0 32.570103 38.407539 82 0 0 32.529771 38.370564 83 0 0 32.499775 38.343789 84 0 0 32.491113 38.336071 85 0 0 32.473498 38.320292 86 0 0 32.461102 38.306594 87 0 0 32.447271 38.290917 88 0 0 32.426861 38.273096 89 0 0 32.393121 38.239038 90 0 0 32.356002 38.207431 91 0 0 32.336029 38.183117 92 0 0 32.298296 38.15009 93 0 0 32.271519 38.12508 94 0 0 32.244801 38.101542 95 0 0 32.201818 38.067595 96 0 0 32.172119 38.042256 97 0 0 32.149161 38.024803 98 0 0 32.159732 38.035393 99 0 0 32.171804 38.043932 100 0 0 32.211234 38.076748 101 0 0 32.257685 38.110819 102 0 0 32.308932 38.150656 103 0 0 32.360235 38.187279 104 0 0 32.400302 38.217502 105 0 0 32.441235 38.243346 106 0 0 32.464909 38.259652 107 0 0 32.487676 38.280526 108 0 0 32.50341 38.290923 109 0 0 32.523822 38.30702 110 0 0 32.520694 38.302228 111 0 0 32.492923 38.280676 112 0 0 32.473389 38.262723 113 0 0 32.428715 38.223328 114 0 0 32.390342 38.194611 115 0 0 32.346682 38.158495 116 0 0 32.308308 38.131284 117 0 0 32.309095 38.137633 118 0 0 32.305276 38.135763 119 0 0 32.307822 38.139839 120 0 0 32.330877 38.159856 121 0 0 32.341098 38.162907 122 0 0 32.357835 38.178325 123 0 0 32.387633 38.202353 124 0 0 32.410187 38.209307 125 0 0 32.43297 38.229764 126 0 0 32.455045 38.243399 127 0 0 32.467772 38.248486 128 0 0 32.457205 38.23897 129 0 0 32.451261 38.234563 130 0 0 32.428476 38.209242 131 0 0 32.417874 38.205355 132 0 0 32.409744 38.194545 133 0 0 32.393951 38.182399 134 0 0 32.402688 38.185237 135 0 0 32.423476 38.194131 136 0 0 32.398766 38.179286 137 0 0 32.410102 38.185956 138 0 0 32.416455 38.194963 139 0 0 32.451805 38.222176 140 0 0 32.442135 38.216438 141 0 0 32.481744 38.248154 142 0 0 32.498074 38.259211 143 0 0 32.521926 38.275053 144 0 0 32.512462 38.269534 145 0 0 32.516362 38.262518 146 0 0 32.514903 38.261568 147 0 0 32.488684 38.23948 148 0 0 32.461132 38.212088 149 0 0 32.428703 38.188704 150 0 0 32.398017 38.160014 151 0 0 32.360106 38.131674 152 0 0 32.352663 38.12825 153 0 0 32.333355 38.113485 154 0 0 32.340284 38.113098 155 0 0 32.344734 38.119013 156 0 0 32.337658 38.112577 157 0 0 32.376265 38.14278 158 0 0 32.42973 38.180894 159 0 0 32.425462 38.187823 160 0 0 32.485405 38.231037 161 0 0 32.531828 38.266656 162 0 0 32.549168 38.27866 163 0 0 32.598862 38.322321 164 0 0 32.607717 38.331539 165 0 0 32.619041 38.341498 166 0 0 32.601189 38.314329 167 0 0 32.622389 38.332663 168 0 0 32.575625 38.284518 169 0 0 32.527527 38.249029 170 0 0 32.52923 38.24667 171 0 0 32.521377 38.237648 172 0 0 32.52552 38.239189 173 0 0 32.536823 38.255343 174 0 0 32.521625 38.243718 175 0 0 32.570524 38.284236 176 0 0 32.590247 38.297612 177 0 0 32.625767 38.342219 178 0 0 32.631854 38.34503 179 0 0 32.682056 38.382056 180 0 0 32.750577 38.448436 181 0 0 32.830054 38.503291 182 0 0 32.841249 38.515712 183 0 0 32.906809 38.571215 184 0 0 32.958036 38.620274 185 0 0 32.979849 38.628366 186 0 0 32.994803 38.648311 187 0 0 33.003602 38.645933 188 0 0 33.022195 38.679905 189 0 0 33.035475 38.686493 190 0 0 33.011308 38.664062 191 0 0 33.010956 38.668526 192 0 0 33.009358 38.68135 193 0 0 32.971787 38.653138 194 0 0 32.966068 38.6472 195 0 0 32.985241 38.67086 196 0 0 32.898987 38.615811 197 0 0 32.942932 38.651896 198 0 0 32.92403 38.652436 199 0 0 32.921734 38.654645 200 0 0 32.878912 38.626614 201 0 0 32.902575 38.649977 202 0 0 32.855914 38.615544 203 0 0 32.884499 38.645229 204 0 0 32.851021 38.62532 205 0 0 32.76284 38.574072 206 0 0 32.76744 38.567692 207 0 0 32.798764 38.615962 208 0 0 32.819665 38.626071 209 0 0 32.750034 38.570989 210 0 0 32.740025 38.572914 211 0 0 32.67679 38.549111 212 0 0 32.608413 38.489509 213 0 0 32.633023 38.511846 214 0 0 32.597811 38.488375 215 0 0 32.588038 38.483477 216 0 0 32.630207 38.512004 217 0 0 32.592712 38.490306 218 0 0 32.587068 38.494721 219 0 0 32.598944 38.503698 220 0 0 32.549915 38.467552 221 0 0 32.525437 38.453784 222 0 0 32.51573 38.454267 223 0 0 32.491412 38.424534 224 0 0 32.556794 38.465393 225 0 0 32.462095 38.418139 226 0 0 32.440719 38.401018 227 0 0 32.356744 38.34142 228 0 0 32.301395 38.291012 229 0 0 32.366592 38.32867 230 0 0 32.284548 38.292844 231 0 0 32.285643 38.287199 232 0 0 32.268803 38.287216 233 0 0 32.244597 38.270097 234 0 0 32.199041 38.258301 235 0 0 32.143936 38.219028 236 0 0 32.129207 38.208696 237 0 0 32.154395 38.207104 238 0 0 32.144192 38.218291 239 0 0 32.13406 38.207275 240 0 0 32.038596 38.186126 241 0 0 31.988292 38.109279 242 0 0 31.987441 38.118088 243 0 0 31.865298 38.046441 244 0 0 31.917855 38.070572 245 0 0 31.833259 38.050657 246 0 0 31.797024 38.010739 247 0 0 31.924583 38.11933 248 0 0 31.794568 37.994557 249 0 0 31.780997 37.996379 250 0 0 31.76997 37.971239 251 0 0 31.735376 37.966291 252 0 0 31.515446 37.781401 253 0 0 31.525183 37.820594 254 0 0 31.527217 37.805165 255 0 0 31.562248 37.865182 256 0 0 31.428791 37.759056 257 0 0 31.643051 37.900558 258 0 0 31.271917 37.673855 259 0 0 31.549842 37.855122 260 0 0 31.469009 37.786366 261 0 0 31.254673 37.635427 262 0 0 31.119495 37.57474 263 0 0 31.041977 37.48946 264 0 0 31.008496 37.518739 265 0 0 31.065249 37.528789 266 0 0 31.027702 37.523637 267 0 0 30.978869 37.497928 268 0 0 31.05933 37.517172 269 0 0 30.68146 37.312842 270 0 0 30.898717 37.396466 271 0 0 30.561129 37.168002 272 0 0 30.674794 37.325923 273 0 0 30.559941 37.232755 274 0 0 30.420015 37.094516 275 0 0 30.421808 37.04773 276 0 0 30.223558 36.988248 277 0 0 30.060206 36.885361 278 0 0 30.198477 36.948512 279 0 0 30.036213 36.874636 280 0 0 29.909663 36.77573 281 0 0 29.880389 36.763097 282 0 0 30.038054 36.848105 283 0 0 29.671478 36.611747 284 0 0 29.562305 36.608688 285 0 0 29.815352 36.714081 286 0 0 29.512277 36.50093 287 0 0 29.579162 36.556849 288 0 0 29.289651 36.378649 289 0 0 29.093571 36.171441 290 0 0 29.156954 36.181678 291 0 0 29.375173 36.418863 292 0 0 29.26289 36.222222 293 0 0 29.251711 36.36654 294 0 0 29.102318 36.181188 295 0 0 29.265717 36.278849 296 0 0 28.846288 36.109753 297 0 0 28.707804 35.872958 298 0 0 29.063158 36.18437 299 0 0 28.027136 35.434841 300 0 0 29.069002 36.215145 301 0 0 28.942889 36.105636 302 0 0 28.81764 35.951132 303 0 0 28.887768 35.978983 304 0 0 28.918883 36.060727 305 0 0 28.534851 35.834519 306 0 0 27.74924 35.22999 307 0 0 28.051613 35.400538 308 0 0 28.242531 35.609842 309 0 0 27.998127 35.314607 310 0 0 28.636364 35.847138 311 0 0 27.659341 35.312088 312 0 0 28.28401 35.731106 313 0 0 28.804124 36.006873 314 0 0 29.091691 36.174785 315 0 0 28.628205 35.744658 316 0 0 27.552542 35.387571 317 0 0 28.474265 35.708333 318 0 0 28.497959 35.688435 319 0 0 29.02765 36.056836 320 0 0 28.934343 35.97138 321 0 0 28.430939 35.839779 322 0 0 27.272727 34.820202 323 0 0 27.006623 34.580574 324 0 0 25.947761 33.927861 325 0 0 27.677966 34.971751 326 0 0 26.368932 34.042071 327 0 0 27.32967 34.882784 328 0 0 26.949367 34.56962 329 0 0 26.969697 35.050505 330 0 0 26.728814 34.813559 331 0 0 25.884615 33.852564 332 0 0 27.266667 35.103704 333 0 0 29.190476 36.484127 334 0 0 25.289474 33.491228 335 0 0 26.272727 33.535354 336 0 0 26.78125 34.822917 337 0 0 23.962963 33.91358 338 0 0 25.5 33.416667 339 0 0 28.181818 35.242424 340 0 0 25.3 33.666667 341 0 0 31.117647 37.294118 342 0 0 30.428571 37.666667 343 0 0 20.583333 30.527778 344 0 0 22.25 31.416667 345 0 0 27.2 35.366667 346 0 0 17.625 29.166667 347 0 0 24.571429 32.047619 348 0 0 31.428571 37.857143 349 0 0 29.333333 35.055556 350 0 0 32.8 38.733333 351 0 0 17.2 25.866667 352 0 0 29.75 37.75 353 0 0 23.25 33.416667 354 0 0 26 33.555556 355 0 0 28.333333 37.555556 356 0 0 25.333333 36.111111 357 0 0 35.333333 40.111111 358 0 0 27.666667 34.777778 359 0 0 32 38.666667 360 0 0 28.666667 37 361 0 0 17.333333 28.444444 362 0 0 15 25.666667 363 0 0 26 36 364 0 0 13 23 365 0 0 7.5 15.166667 366 0 0 36 41