## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5380-Z0048-CTGCCAGACTGTGAT/441525-L5380-Z0048-CTGCCAGACTGTGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5380-Z0048-CTGCCAGACTGTGAT/441525-L5380-Z0048-CTGCCAGACTGTGAT_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 02:54:32 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 999244 999244 137 136977587 136977587 132174693 132174693 122972326 122972326 0 0 0.964937 0.897755 0 0.964937 0.897755 0 410932761 410932761 404608299 404608299 389886579 389886579 365055100 365055100 0.984609 0.948784 0.888357 0.984609 0.948784 0.888357 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 888 1 35.980958 40.986725 1 11058 0 35.974728 40.981909 2 13353 4569 35.987271 40.989928 3 34143 1228 35.967746 40.974176 4 54520 46999 35.984519 40.987373 5 108234 16633 35.991859 40.993374 6 107205 122520 35.970545 40.976523 7 191392 154694 35.97735 40.984421 8 188699 144675 35.986759 40.989331 9 234494 106333 35.949679 40.957854 10 243478 497162 35.884753 40.928228 11 289765 60235 35.928178 40.947239 12 343900 691736 35.265628 40.382482 13 346586 200813 33.835036 39.654547 14 445414 966144 35.881952 40.929238 15 367854 370354 35.800154 40.859464 16 380031 428787 35.749556 40.777795 17 514721 1095534 35.876758 40.894302 18 549246 721578 35.716638 40.768861 19 377913 694467 35.742772 40.809185 20 511947 1001259 35.906667 40.937338 21 664922 1375726 35.824247 40.872585 22 328686 557589 35.591627 40.722259 23 1041953 1225918 35.321273 40.538594 24 590885 1207624 35.337292 40.552877 25 539267 487700 35.350584 40.560061 26 1761398 2497593 35.285064 40.509544 27 366418 902599 35.305502 40.529645 28 954100 391058 35.321153 40.540989 29 2442791 5074654 35.320151 40.539438 30 780529 40409 35.319745 40.53931 31 2353693 846409 35.308546 40.529297 32 1608988 5411849 35.296469 40.518927 33 853857 121699 35.30279 40.524747 34 2482823 2663787 35.297458 40.521907 35 2262119 3857490 35.311463 40.531156 36 112630317 2133262 35.335607 40.546455 37 0 4300079 35.334804 40.547434 38 0 385927 35.32645 40.542458 39 0 5070568 35.322158 40.539434 40 0 1 35.316074 40.533611 41 0 365055099 35.303839 40.525582 42 0 0 35.298671 40.520052 43 0 0 35.305868 40.525737 44 0 0 35.30581 40.525896 45 0 0 35.314068 40.531525 46 0 0 35.304497 40.524713 47 0 0 35.301707 40.522779 48 0 0 35.288056 40.514603 49 0 0 35.283748 40.511113 50 0 0 35.284716 40.512825 51 0 0 35.275644 40.505005 52 0 0 35.253499 40.489933 53 0 0 35.240814 40.484543 54 0 0 35.245559 40.485995 55 0 0 35.239266 40.482156 56 0 0 35.210292 40.463917 57 0 0 35.212446 40.460616 58 0 0 35.187902 40.441996 59 0 0 35.164815 40.424486 60 0 0 35.119752 40.39287 61 0 0 35.080669 40.36171 62 0 0 35.046897 40.336024 63 0 0 34.991371 40.295265 64 0 0 34.937131 40.254392 65 0 0 34.882172 40.212625 66 0 0 34.807602 40.157381 67 0 0 34.736191 40.103571 68 0 0 34.655033 40.04166 69 0 0 34.566617 39.975041 70 0 0 34.460999 39.89251 71 0 0 34.371431 39.818035 72 0 0 34.268573 39.736515 73 0 0 34.158813 39.647641 74 0 0 34.056662 39.56845 75 0 0 33.957777 39.491834 76 0 0 33.855762 39.41304 77 0 0 33.766961 39.346 78 0 0 33.679794 39.27779 79 0 0 33.593687 39.209864 80 0 0 33.528165 39.157524 81 0 0 33.454621 39.097418 82 0 0 33.404395 39.053433 83 0 0 33.353162 39.010893 84 0 0 33.313717 38.980724 85 0 0 33.278657 38.952737 86 0 0 33.251829 38.925689 87 0 0 33.215607 38.895521 88 0 0 33.175457 38.864014 89 0 0 33.124512 38.820096 90 0 0 33.099701 38.796143 91 0 0 33.050903 38.75394 92 0 0 33.02013 38.725934 93 0 0 32.991831 38.700073 94 0 0 32.955928 38.670982 95 0 0 32.921191 38.641265 96 0 0 32.907224 38.625894 97 0 0 32.886656 38.610593 98 0 0 32.879544 38.605711 99 0 0 32.896319 38.618185 100 0 0 32.919132 38.635089 101 0 0 32.95024 38.65712 102 0 0 32.990556 38.688059 103 0 0 33.013235 38.704883 104 0 0 33.038057 38.722759 105 0 0 33.066783 38.740372 106 0 0 33.075336 38.746577 107 0 0 33.092753 38.756485 108 0 0 33.095545 38.761463 109 0 0 33.097311 38.762316 110 0 0 33.083406 38.751747 111 0 0 33.065941 38.737748 112 0 0 33.038324 38.710558 113 0 0 32.976698 38.65998 114 0 0 32.939856 38.62851 115 0 0 32.886287 38.587617 116 0 0 32.871784 38.576626 117 0 0 32.845273 38.559653 118 0 0 32.846072 38.561981 119 0 0 32.840279 38.560523 120 0 0 32.845531 38.564967 121 0 0 32.847315 38.565731 122 0 0 32.858913 38.571371 123 0 0 32.862172 38.576643 124 0 0 32.868526 38.575198 125 0 0 32.901775 38.599237 126 0 0 32.907687 38.602985 127 0 0 32.901807 38.593427 128 0 0 32.898662 38.592133 129 0 0 32.887971 38.578562 130 0 0 32.872964 38.562533 131 0 0 32.858955 38.554333 132 0 0 32.854284 38.549947 133 0 0 32.84783 38.54316 134 0 0 32.852553 38.54604 135 0 0 32.841897 38.533905 136 0 0 32.836065 38.526547 137 0 0 32.82119 38.517192 138 0 0 32.831703 38.528184 139 0 0 32.84831 38.540913 140 0 0 32.867676 38.558336 141 0 0 32.887892 38.574304 142 0 0 32.895814 38.573569 143 0 0 32.90204 38.577616 144 0 0 32.895273 38.573095 145 0 0 32.885692 38.565326 146 0 0 32.880279 38.557477 147 0 0 32.860978 38.537839 148 0 0 32.828795 38.512482 149 0 0 32.820861 38.508669 150 0 0 32.78348 38.478388 151 0 0 32.757928 38.456591 152 0 0 32.728297 38.43551 153 0 0 32.718792 38.42219 154 0 0 32.737 38.441266 155 0 0 32.711162 38.416641 156 0 0 32.736723 38.435019 157 0 0 32.748911 38.447456 158 0 0 32.761359 38.457071 159 0 0 32.82137 38.503773 160 0 0 32.834571 38.51197 161 0 0 32.840159 38.514979 162 0 0 32.891951 38.558682 163 0 0 32.900678 38.569315 164 0 0 32.912556 38.570832 165 0 0 32.911532 38.57587 166 0 0 32.89634 38.559334 167 0 0 32.901101 38.558985 168 0 0 32.868929 38.525391 169 0 0 32.817464 38.484888 170 0 0 32.805944 38.477361 171 0 0 32.764636 38.438822 172 0 0 32.779027 38.453175 173 0 0 32.791236 38.466573 174 0 0 32.782806 38.458842 175 0 0 32.79621 38.470275 176 0 0 32.81748 38.49126 177 0 0 32.82466 38.496707 178 0 0 32.880975 38.545387 179 0 0 32.917288 38.581066 180 0 0 32.931613 38.586235 181 0 0 32.976463 38.6296 182 0 0 33.025702 38.674902 183 0 0 33.055043 38.696195 184 0 0 33.111788 38.746299 185 0 0 33.162637 38.777948 186 0 0 33.155237 38.77594 187 0 0 33.183246 38.800598 188 0 0 33.184795 38.800229 189 0 0 33.181273 38.798071 190 0 0 33.192471 38.80664 191 0 0 33.158643 38.791639 192 0 0 33.165741 38.797828 193 0 0 33.121327 38.772707 194 0 0 33.129308 38.78465 195 0 0 33.120143 38.779777 196 0 0 33.106763 38.774113 197 0 0 33.097578 38.769737 198 0 0 33.080963 38.762719 199 0 0 33.080975 38.772414 200 0 0 33.071238 38.770815 201 0 0 33.077118 38.778442 202 0 0 33.034909 38.753679 203 0 0 32.996414 38.736846 204 0 0 33.015185 38.754269 205 0 0 32.968671 38.728401 206 0 0 32.983782 38.743544 207 0 0 32.96825 38.736158 208 0 0 32.954946 38.726541 209 0 0 32.92946 38.710814 210 0 0 32.93375 38.722524 211 0 0 32.863973 38.674536 212 0 0 32.850279 38.676327 213 0 0 32.854154 38.67544 214 0 0 32.817275 38.652214 215 0 0 32.766411 38.616291 216 0 0 32.784232 38.637889 217 0 0 32.761006 38.617457 218 0 0 32.713731 38.587818 219 0 0 32.721167 38.600366 220 0 0 32.687801 38.569803 221 0 0 32.677643 38.563276 222 0 0 32.658082 38.563093 223 0 0 32.669129 38.569644 224 0 0 32.588074 38.503771 225 0 0 32.595144 38.522139 226 0 0 32.56194 38.485753 227 0 0 32.475527 38.428528 228 0 0 32.493939 38.450466 229 0 0 32.51412 38.462767 230 0 0 32.472964 38.430523 231 0 0 32.372606 38.366662 232 0 0 32.408476 38.400566 233 0 0 32.35786 38.362859 234 0 0 32.359816 38.37786 235 0 0 32.404166 38.406525 236 0 0 32.33306 38.366124 237 0 0 32.331305 38.350309 238 0 0 32.27609 38.316234 239 0 0 32.19937 38.272032 240 0 0 32.27624 38.320816 241 0 0 32.147047 38.242639 242 0 0 32.138505 38.241165 243 0 0 32.173244 38.25328 244 0 0 32.066295 38.201716 245 0 0 31.999272 38.160197 246 0 0 31.951001 38.12218 247 0 0 31.924168 38.101369 248 0 0 31.958019 38.110857 249 0 0 31.864953 38.060852 250 0 0 31.804186 38.000286 251 0 0 31.869962 38.081123 252 0 0 31.890854 38.094537 253 0 0 31.803634 38.030015 254 0 0 31.626454 37.926226 255 0 0 31.548041 37.894638 256 0 0 31.553586 37.849155 257 0 0 31.491069 37.83525 258 0 0 31.465857 37.823526 259 0 0 31.504307 37.842745 260 0 0 31.517748 37.839668 261 0 0 31.497555 37.823967 262 0 0 31.409483 37.77939 263 0 0 31.441924 37.810924 264 0 0 31.338443 37.736678 265 0 0 31.282742 37.720182 266 0 0 31.140356 37.596122 267 0 0 31.02536 37.521169 268 0 0 31.020693 37.523867 269 0 0 31.004277 37.517335 270 0 0 31.172287 37.607281 271 0 0 30.973607 37.524567 272 0 0 30.787967 37.352946 273 0 0 30.798984 37.367662 274 0 0 30.657764 37.309593 275 0 0 30.519735 37.176448 276 0 0 30.662405 37.271585 277 0 0 30.435276 37.10696 278 0 0 30.398767 37.090841 279 0 0 30.159372 36.980324 280 0 0 30.271156 37.015655 281 0 0 30.068741 36.949418 282 0 0 30.188338 36.993556 283 0 0 29.981693 36.841764 284 0 0 29.952483 36.800088 285 0 0 29.776965 36.719122 286 0 0 29.801656 36.712407 287 0 0 29.575988 36.53881 288 0 0 29.586973 36.560221 289 0 0 29.526723 36.520333 290 0 0 29.578226 36.595363 291 0 0 29.365533 36.387092 292 0 0 29.413119 36.44179 293 0 0 29.471345 36.503761 294 0 0 29.331379 36.407442 295 0 0 28.961482 36.162197 296 0 0 29.323642 36.34804 297 0 0 29.158734 36.250908 298 0 0 28.899586 36.086529 299 0 0 28.88676 36.073848 300 0 0 28.894785 36.04849 301 0 0 28.746088 35.932716 302 0 0 28.633277 35.929636 303 0 0 29.095373 36.232898 304 0 0 28.362378 35.651458 305 0 0 28.8499 36.155422 306 0 0 28.71741 36 307 0 0 28.68328 35.934904 308 0 0 28.743039 35.934538 309 0 0 28.600313 35.889005 310 0 0 28.336134 35.780579 311 0 0 28.227488 35.651066 312 0 0 28.587413 35.808222 313 0 0 28.278655 35.636239 314 0 0 28.589153 35.807826 315 0 0 28.71257 35.883106 316 0 0 28.274849 35.484875 317 0 0 28.650899 35.878272 318 0 0 28.328907 35.497446 319 0 0 28.269575 35.603281 320 0 0 28.244499 35.413203 321 0 0 27.621333 35.287556 322 0 0 27.592047 35.116348 323 0 0 28.536232 35.733763 324 0 0 27.585145 35.185386 325 0 0 27.834 35.337333 326 0 0 27.597826 35.063768 327 0 0 27.6 35.02381 328 0 0 27.817708 35.18316 329 0 0 27.29661 35.074388 330 0 0 27.996904 35.462332 331 0 0 28.827119 35.910734 332 0 0 27.951311 35.322097 333 0 0 28.155462 35.52381 334 0 0 27.599057 35.290881 335 0 0 29.315217 36.422101 336 0 0 28.109091 35.387879 337 0 0 27.880795 35.298013 338 0 0 27.437037 35.239506 339 0 0 29.247863 36.108262 340 0 0 28.871287 36.052805 341 0 0 28.695652 36.086957 342 0 0 28.115385 35.495726 343 0 0 29.256757 36.342342 344 0 0 29.075758 36.580808 345 0 0 27.362069 35.178161 346 0 0 26.06 34.446667 347 0 0 29.04878 36.593496 348 0 0 27.342857 35.580952 349 0 0 29.551724 36.574713 350 0 0 25.769231 34.74359 351 0 0 29.88 36.293333 352 0 0 28.842105 35.77193 353 0 0 27.882353 35.45098 354 0 0 30.066667 36.666667 355 0 0 26.214286 33.309524 356 0 0 29.538462 37.051282 357 0 0 32.545455 39.121212 358 0 0 27.8 35.366667 359 0 0 26.666667 34.888889 360 0 0 24.444444 33.074074 361 0 0 28.777778 36.111111 362 0 0 18.25 27.375 363 0 0 24.625 35.5 364 0 0 28.125 36.125 365 0 0 23.428571 30.333333 366 0 0 29 37.714286 367 0 0 34.25 40 368 0 0 24 33.111111 369 0 0 29.333333 36.333333 370 0 0 32.5 39 371 0 0 26 36 372 0 0 28 34.333333 373 0 0 28 34.333333 374 0 0 36 41 375 0 0 36 41 376 0 0 36 41 377 0 0 36 41 378 0 0 13 27 379 0 0 12 20.666667 380 0 0 35 39.666667 381 0 0 23 35 382 0 0 23 35 383 0 0 17 24.333333 384 0 0 36 41 385 0 0 28 34 386 0 0 29 35 387 0 0 28 34