## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5402-Z0091-CACTTCTGCGATGAT/441525-L5402-Z0091-CACTTCTGCGATGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5402-Z0091-CACTTCTGCGATGAT/441525-L5402-Z0091-CACTTCTGCGATGAT_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 02:56:33 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 1000946 1000946 124 124213847 124213847 119311077 119311077 110238526 110238526 0 0 0.96053 0.88749 0 0.96053 0.88749 0 372641541 372641541 366154995 366154995 351574196 351574196 327685310 327685310 0.982593 0.943465 0.879358 0.982593 0.943465 0.879358 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 840 0 35.993879 40.995248 1 11154 2 35.985761 40.990242 2 13109 4185 35.992515 40.993803 3 34255 1149 35.979675 40.983586 4 54103 47449 35.991618 40.993142 5 107357 17260 35.995089 40.996079 6 109457 121350 35.962488 40.965928 7 190666 154723 35.97004 40.978718 8 191574 146618 35.990045 40.99195 9 233339 109113 35.966864 40.972242 10 249980 493493 35.895682 40.934821 11 298047 60270 35.936664 40.953218 12 357475 702337 35.207792 40.335075 13 357358 206171 33.719259 39.585035 14 467222 1000034 35.900198 40.940465 15 373872 371322 35.835743 40.883157 16 399422 460341 35.803153 40.82554 17 522937 1134544 35.902756 40.918248 18 555936 730884 35.74745 40.790627 19 374667 725301 35.749938 40.815001 20 495464 1021151 35.90583 40.938592 21 651626 1356310 35.851162 40.892768 22 318230 569136 35.618837 40.736037 23 1014862 1184921 35.342524 40.551413 24 564375 1163217 35.327533 40.544273 25 537190 467801 35.328371 40.544329 26 1737446 2511663 35.263332 40.497425 27 351907 849204 35.263029 40.498454 28 948261 359404 35.28535 40.513368 29 2453190 5097992 35.28161 40.510024 30 713745 36722 35.266204 40.498785 31 2286524 764691 35.255225 40.490718 32 1513918 5437762 35.247712 40.484904 33 786633 114543 35.251071 40.486082 34 2351508 2429445 35.240493 40.480062 35 2109866 3792292 35.251292 40.487304 36 100476332 1966478 35.270507 40.50012 37 0 4178348 35.269507 40.501965 38 0 333140 35.263116 40.49699 39 0 4835465 35.259889 40.493724 40 0 1 35.259566 40.492423 41 0 327685309 35.24278 40.481361 42 0 0 35.237983 40.476706 43 0 0 35.23966 40.477917 44 0 0 35.25083 40.485672 45 0 0 35.250911 40.48634 46 0 0 35.244199 40.483241 47 0 0 35.235467 40.475978 48 0 0 35.222855 40.467088 49 0 0 35.219673 40.463844 50 0 0 35.21262 40.459724 51 0 0 35.188927 40.44343 52 0 0 35.181837 40.436053 53 0 0 35.157686 40.41973 54 0 0 35.14619 40.4112 55 0 0 35.116626 40.389989 56 0 0 35.074781 40.35924 57 0 0 35.042103 40.33683 58 0 0 34.992944 40.299849 59 0 0 34.925622 40.250197 60 0 0 34.856683 40.198592 61 0 0 34.776632 40.138973 62 0 0 34.67429 40.060716 63 0 0 34.577751 39.983559 64 0 0 34.46534 39.898364 65 0 0 34.344187 39.806493 66 0 0 34.207516 39.705222 67 0 0 34.067264 39.597769 68 0 0 33.928247 39.495009 69 0 0 33.775545 39.373967 70 0 0 33.612084 39.244245 71 0 0 33.462557 39.125743 72 0 0 33.307699 38.996357 73 0 0 33.172316 38.887982 74 0 0 33.043011 38.78471 75 0 0 32.934364 38.702679 76 0 0 32.826584 38.618806 77 0 0 32.753506 38.565231 78 0 0 32.686196 38.514452 79 0 0 32.629694 38.46581 80 0 0 32.596921 38.435849 81 0 0 32.576209 38.416883 82 0 0 32.564078 38.402615 83 0 0 32.563708 38.396989 84 0 0 32.56583 38.395491 85 0 0 32.566222 38.393897 86 0 0 32.548694 38.37549 87 0 0 32.535836 38.363753 88 0 0 32.507436 38.339703 89 0 0 32.478284 38.311194 90 0 0 32.4504 38.283201 91 0 0 32.40652 38.243092 92 0 0 32.369165 38.214825 93 0 0 32.328762 38.179408 94 0 0 32.291289 38.149617 95 0 0 32.254037 38.118603 96 0 0 32.216825 38.090224 97 0 0 32.232325 38.101106 98 0 0 32.21024 38.086414 99 0 0 32.245455 38.110914 100 0 0 32.300678 38.158422 101 0 0 32.359227 38.200794 102 0 0 32.405339 38.23817 103 0 0 32.485022 38.296402 104 0 0 32.519369 38.319873 105 0 0 32.56238 38.351539 106 0 0 32.588016 38.36781 107 0 0 32.606813 38.382775 108 0 0 32.614677 38.388159 109 0 0 32.627049 38.397286 110 0 0 32.632422 38.399552 111 0 0 32.601376 38.373678 112 0 0 32.579583 38.357373 113 0 0 32.519117 38.306911 114 0 0 32.472166 38.273813 115 0 0 32.441859 38.24694 116 0 0 32.426297 38.237639 117 0 0 32.41939 38.230648 118 0 0 32.438984 38.249186 119 0 0 32.423882 38.237849 120 0 0 32.439216 38.250732 121 0 0 32.462935 38.269804 122 0 0 32.474477 38.278766 123 0 0 32.49526 38.295022 124 0 0 32.522806 38.307882 125 0 0 32.545951 38.324912 126 0 0 32.571297 38.336332 127 0 0 32.565165 38.329848 128 0 0 32.562542 38.322407 129 0 0 32.550698 38.314219 130 0 0 32.506355 38.273944 131 0 0 32.507134 38.273187 132 0 0 32.508891 38.274046 133 0 0 32.508384 38.273847 134 0 0 32.500478 38.267557 135 0 0 32.493868 38.261565 136 0 0 32.501678 38.264569 137 0 0 32.512369 38.277599 138 0 0 32.50843 38.275837 139 0 0 32.521787 38.288153 140 0 0 32.556635 38.308709 141 0 0 32.602153 38.343259 142 0 0 32.603974 38.349458 143 0 0 32.611867 38.353814 144 0 0 32.622941 38.358388 145 0 0 32.619128 38.356224 146 0 0 32.599226 38.336939 147 0 0 32.57174 38.309003 148 0 0 32.548007 38.284022 149 0 0 32.523694 38.261684 150 0 0 32.482975 38.236546 151 0 0 32.453406 38.217276 152 0 0 32.449348 38.213583 153 0 0 32.456 38.213759 154 0 0 32.474514 38.229703 155 0 0 32.430426 38.192729 156 0 0 32.480739 38.233518 157 0 0 32.513874 38.269003 158 0 0 32.530055 38.270338 159 0 0 32.581139 38.309333 160 0 0 32.585095 38.315635 161 0 0 32.633808 38.354565 162 0 0 32.650925 38.365274 163 0 0 32.664629 38.377548 164 0 0 32.681851 38.396013 165 0 0 32.672187 38.381059 166 0 0 32.70924 38.403685 167 0 0 32.684216 38.387365 168 0 0 32.652454 38.354663 169 0 0 32.652492 38.359989 170 0 0 32.631224 38.339485 171 0 0 32.61495 38.322915 172 0 0 32.620875 38.328948 173 0 0 32.627979 38.341442 174 0 0 32.655447 38.357323 175 0 0 32.699959 38.398232 176 0 0 32.668158 38.372584 177 0 0 32.732097 38.431597 178 0 0 32.772691 38.460549 179 0 0 32.78855 38.473879 180 0 0 32.83829 38.516877 181 0 0 32.928543 38.59108 182 0 0 32.91858 38.58648 183 0 0 32.999511 38.658088 184 0 0 33.010284 38.664641 185 0 0 33.055206 38.695161 186 0 0 33.050389 38.691462 187 0 0 33.099582 38.739296 188 0 0 33.106612 38.744562 189 0 0 33.100674 38.748359 190 0 0 33.091611 38.741905 191 0 0 33.066982 38.724022 192 0 0 33.07496 38.732797 193 0 0 33.067682 38.731556 194 0 0 33.005405 38.688945 195 0 0 33.030043 38.70972 196 0 0 33.015281 38.70505 197 0 0 33.010139 38.711592 198 0 0 32.99456 38.702882 199 0 0 33.025824 38.732836 200 0 0 32.977562 38.708793 201 0 0 32.933989 38.678228 202 0 0 32.997765 38.731995 203 0 0 32.929271 38.68787 204 0 0 32.886359 38.668157 205 0 0 32.846237 38.649929 206 0 0 32.865709 38.662165 207 0 0 32.914284 38.702861 208 0 0 32.8826 38.68235 209 0 0 32.865864 38.674754 210 0 0 32.809518 38.636537 211 0 0 32.861009 38.668332 212 0 0 32.79052 38.62249 213 0 0 32.740776 38.583231 214 0 0 32.753963 38.596925 215 0 0 32.726155 38.585769 216 0 0 32.690439 38.561716 217 0 0 32.668835 38.570333 218 0 0 32.657169 38.53906 219 0 0 32.620973 38.530606 220 0 0 32.660865 38.549392 221 0 0 32.586237 38.501294 222 0 0 32.585325 38.509077 223 0 0 32.587597 38.496486 224 0 0 32.562689 38.493884 225 0 0 32.523593 38.479621 226 0 0 32.550807 38.475231 227 0 0 32.515252 38.453489 228 0 0 32.464454 38.449702 229 0 0 32.458239 38.419205 230 0 0 32.399069 38.391822 231 0 0 32.374709 38.35693 232 0 0 32.386203 38.377946 233 0 0 32.372915 38.369047 234 0 0 32.345752 38.348782 235 0 0 32.335172 38.339674 236 0 0 32.283835 38.309875 237 0 0 32.275844 38.326785 238 0 0 32.132159 38.224748 239 0 0 32.192788 38.250986 240 0 0 32.137593 38.253888 241 0 0 32.038371 38.177457 242 0 0 32.079551 38.191719 243 0 0 32.101324 38.220521 244 0 0 32.114966 38.225948 245 0 0 32.113062 38.227294 246 0 0 31.955978 38.122318 247 0 0 31.977265 38.142918 248 0 0 32.04387 38.173465 249 0 0 31.94812 38.106253 250 0 0 31.894496 38.0895 251 0 0 31.794364 38.00668 252 0 0 31.875313 38.07699 253 0 0 31.818698 38.016033 254 0 0 31.531734 37.807296 255 0 0 31.741861 37.963811 256 0 0 31.738722 37.973148 257 0 0 31.528234 37.805868 258 0 0 31.497035 37.837978 259 0 0 31.474543 37.833791 260 0 0 31.463361 37.827292 261 0 0 31.333387 37.720291 262 0 0 31.547607 37.877574 263 0 0 31.284742 37.695243 264 0 0 31.236128 37.655231 265 0 0 31.101543 37.588805 266 0 0 31.073067 37.575163 267 0 0 31.311317 37.745458 268 0 0 31.292207 37.706891 269 0 0 30.995222 37.56885 270 0 0 30.831018 37.425351 271 0 0 30.817706 37.410074 272 0 0 30.887384 37.443155 273 0 0 30.763285 37.355072 274 0 0 30.647364 37.256647 275 0 0 30.43786 37.084313 276 0 0 30.34114 37.078306 277 0 0 30.332768 37.073383 278 0 0 30.137606 36.957609 279 0 0 30.147395 36.889369 280 0 0 30.310408 37.082636 281 0 0 30.169033 37.002947 282 0 0 29.983747 36.821947 283 0 0 29.730856 36.672811 284 0 0 29.894798 36.753263 285 0 0 29.648428 36.64611 286 0 0 29.725374 36.658042 287 0 0 29.732091 36.655852 288 0 0 29.627614 36.584135 289 0 0 29.747841 36.713874 290 0 0 29.435109 36.481349 291 0 0 29.725389 36.605107 292 0 0 29.197993 36.280201 293 0 0 28.990338 36.239399 294 0 0 29.274633 36.332774 295 0 0 29.014873 36.182852 296 0 0 28.718993 36.036156 297 0 0 28.836998 36.02645 298 0 0 28.837513 36.065196 299 0 0 29.047544 36.191935 300 0 0 28.951138 36.097723 301 0 0 28.946418 36.119394 302 0 0 28.756261 35.984728 303 0 0 29.050064 36.123235 304 0 0 28.699454 35.939208 305 0 0 28.80942 36.052415 306 0 0 28.961832 36.151654 307 0 0 28.437043 35.748172 308 0 0 28.494363 35.753686 309 0 0 28.888579 36.040854 310 0 0 28.565907 35.778989 311 0 0 28.801303 36.008686 312 0 0 27.895858 35.371598 313 0 0 27.826362 35.231939 314 0 0 28.051984 35.515732 315 0 0 28.18209 35.625871 316 0 0 28.216039 35.617021 317 0 0 27.819643 35.270238 318 0 0 27.930097 35.454369 319 0 0 27.87957 35.325448 320 0 0 28.238095 35.476984 321 0 0 28.414365 35.912523 322 0 0 27.842593 35.230453 323 0 0 28.869863 36.119863 324 0 0 27.700389 35.101167 325 0 0 28.411765 35.676471 326 0 0 27.733333 35.152381 327 0 0 27.466321 34.963731 328 0 0 28.017751 35.737673 329 0 0 28.564935 35.785714 330 0 0 28.573427 35.895105 331 0 0 28.015504 35.49354 332 0 0 28.293103 35.413793 333 0 0 27.472727 34.866667 334 0 0 27.762376 35.346535 335 0 0 27.606383 35.074468 336 0 0 26.795181 34.417671 337 0 0 26.813333 34.315556 338 0 0 27.441176 35.034314 339 0 0 28.730159 35.719577 340 0 0 24.381818 32.660606 341 0 0 25.816327 34.006803 342 0 0 28.636364 35.787879 343 0 0 28.763158 35.973684 344 0 0 28 35.688172 345 0 0 25.814815 34.296296 346 0 0 29.15 35.833333 347 0 0 25.928571 32.785714 348 0 0 28.75 35.388889 349 0 0 29.166667 37.388889 350 0 0 23.777778 32.777778 351 0 0 27.142857 35.47619 352 0 0 30.166667 38 353 0 0 28.4 35.2 354 0 0 28.333333 37 355 0 0 18.666667 30.777778 356 0 0 21.666667 31.555556 357 0 0 21.666667 31.666667 358 0 0 24 32.666667 359 0 0 23 28.666667 360 0 0 30.5 37 361 0 0 36 40.333333 362 0 0 1 16.333333 363 0 0 36 41 364 0 0 7 20.333333 365 0 0 20 31.333333 366 0 0 16 26.333333 367 0 0 31 38 368 0 0 16 26.333333