## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5399-Z0088-CTATCATCCAGTGAT/441525-L5399-Z0088-CTATCATCCAGTGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5399-Z0088-CTATCATCCAGTGAT/441525-L5399-Z0088-CTATCATCCAGTGAT_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 02:59:57 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 1001238 1001238 128 129126218 129126218 124239615 124239615 115181574 115181574 0 0 0.962156 0.892008 0 0.962156 0.892008 0 387378654 387378654 380886161 380886161 366383665 366383665 342288573 342288573 0.98324 0.945802 0.883602 0.98324 0.945802 0.883602 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 826 0 35.993075 40.994691 1 11117 0 35.986214 40.990512 2 13258 4292 35.994298 40.995175 3 34329 1242 35.980178 40.983977 4 55388 46866 35.991289 40.992947 5 108967 17003 35.995126 40.996029 6 112371 122447 35.974954 40.97914 7 191401 155096 35.978956 40.985439 8 192701 148423 35.98938 40.991523 9 235428 108165 35.960353 40.966694 10 246853 503403 35.908658 40.941688 11 297064 59830 35.942666 40.958668 12 355424 701440 35.258885 40.376065 13 355025 211091 33.788536 39.628001 14 464694 1001412 35.901329 40.94026 15 372365 375631 35.819168 40.871944 16 394839 460203 35.778337 40.802331 17 518210 1135467 35.892272 40.908508 18 555370 726194 35.69773 40.751437 19 370973 714288 35.72652 40.796894 20 501180 1010489 35.903263 40.937605 21 647500 1350809 35.848945 40.89104 22 316908 561884 35.630529 40.744162 23 1024611 1182162 35.363265 40.563296 24 564152 1162406 35.344928 40.5538 25 533697 466279 35.352757 40.55906 26 1744096 2518914 35.295845 40.518452 27 348205 848855 35.292185 40.517779 28 945877 359923 35.304795 40.526274 29 2431815 5040775 35.301401 40.523033 30 725697 39568 35.289461 40.516082 31 2270160 771220 35.277643 40.505559 32 1545145 5417759 35.274421 40.502647 33 807177 118435 35.269476 40.499152 34 2388807 2472908 35.265677 40.497921 35 2151601 3810095 35.274723 40.503536 36 105292987 1999672 35.297375 40.52007 37 0 4213173 35.300813 40.522625 38 0 362129 35.286328 40.513812 39 0 4890133 35.284889 40.511074 40 0 0 35.276719 40.505724 41 0 342288573 35.265431 40.496389 42 0 0 35.259668 40.492115 43 0 0 35.261556 40.493832 44 0 0 35.268257 40.498708 45 0 0 35.272945 40.500419 46 0 0 35.266244 40.495818 47 0 0 35.257718 40.489924 48 0 0 35.249885 40.485417 49 0 0 35.240503 40.47859 50 0 0 35.23382 40.474235 51 0 0 35.219905 40.464655 52 0 0 35.20822 40.454942 53 0 0 35.190758 40.444369 54 0 0 35.178273 40.434033 55 0 0 35.165826 40.424682 56 0 0 35.130044 40.400906 57 0 0 35.111384 40.386557 58 0 0 35.069604 40.356672 59 0 0 35.019672 40.320837 60 0 0 34.97165 40.284735 61 0 0 34.919491 40.244294 62 0 0 34.849456 40.190208 63 0 0 34.775241 40.132694 64 0 0 34.686341 40.064764 65 0 0 34.604454 40.002372 66 0 0 34.495815 39.923628 67 0 0 34.389703 39.843669 68 0 0 34.26459 39.74939 69 0 0 34.134532 39.649201 70 0 0 34.000296 39.542449 71 0 0 33.865825 39.434723 72 0 0 33.724233 39.319572 73 0 0 33.583788 39.206991 74 0 0 33.457348 39.105677 75 0 0 33.330295 39.010045 76 0 0 33.216445 38.922931 77 0 0 33.119766 38.849938 78 0 0 33.037707 38.788999 79 0 0 32.956327 38.722295 80 0 0 32.890149 38.664632 81 0 0 32.847103 38.62988 82 0 0 32.807139 38.588785 83 0 0 32.790699 38.575488 84 0 0 32.778704 38.563822 85 0 0 32.768568 38.552143 86 0 0 32.760441 38.544362 87 0 0 32.740609 38.526422 88 0 0 32.705876 38.492363 89 0 0 32.679409 38.472265 90 0 0 32.64533 38.437103 91 0 0 32.629876 38.420327 92 0 0 32.599481 38.391665 93 0 0 32.560591 38.359487 94 0 0 32.53172 38.335028 95 0 0 32.497207 38.307367 96 0 0 32.47696 38.291354 97 0 0 32.458336 38.275109 98 0 0 32.456945 38.275383 99 0 0 32.475683 38.294351 100 0 0 32.52364 38.32917 101 0 0 32.573228 38.369448 102 0 0 32.636729 38.415175 103 0 0 32.687551 38.450646 104 0 0 32.734628 38.486059 105 0 0 32.764145 38.509261 106 0 0 32.794287 38.526863 107 0 0 32.817735 38.545657 108 0 0 32.832812 38.55764 109 0 0 32.837673 38.564625 110 0 0 32.837351 38.56255 111 0 0 32.834871 38.561324 112 0 0 32.808841 38.537598 113 0 0 32.762506 38.496905 114 0 0 32.718203 38.461654 115 0 0 32.686618 38.438527 116 0 0 32.671223 38.425656 117 0 0 32.64891 38.409584 118 0 0 32.661868 38.422425 119 0 0 32.669566 38.43055 120 0 0 32.674233 38.441097 121 0 0 32.69139 38.449075 122 0 0 32.699271 38.455743 123 0 0 32.720492 38.470799 124 0 0 32.740738 38.485784 125 0 0 32.761672 38.493 126 0 0 32.808045 38.529713 127 0 0 32.800966 38.517685 128 0 0 32.797674 38.516968 129 0 0 32.78926 38.506074 130 0 0 32.781719 38.497681 131 0 0 32.779192 38.495298 132 0 0 32.770198 38.486209 133 0 0 32.759687 38.473433 134 0 0 32.771375 38.485845 135 0 0 32.761648 38.473541 136 0 0 32.746991 38.465035 137 0 0 32.744815 38.461111 138 0 0 32.725738 38.448576 139 0 0 32.748698 38.470926 140 0 0 32.768936 38.48185 141 0 0 32.793043 38.506059 142 0 0 32.815352 38.519473 143 0 0 32.815512 38.518383 144 0 0 32.837052 38.535014 145 0 0 32.807131 38.509166 146 0 0 32.789344 38.488639 147 0 0 32.773964 38.47368 148 0 0 32.749634 38.453467 149 0 0 32.705634 38.417423 150 0 0 32.675336 38.396412 151 0 0 32.627007 38.35731 152 0 0 32.657011 38.37856 153 0 0 32.625185 38.350321 154 0 0 32.623084 38.357316 155 0 0 32.613393 38.345387 156 0 0 32.631937 38.350963 157 0 0 32.635349 38.361722 158 0 0 32.644626 38.366686 159 0 0 32.685806 38.396126 160 0 0 32.720419 38.421196 161 0 0 32.760698 38.454941 162 0 0 32.779028 38.467171 163 0 0 32.790081 38.479274 164 0 0 32.798577 38.48574 165 0 0 32.791104 38.479352 166 0 0 32.789408 38.468892 167 0 0 32.775102 38.461048 168 0 0 32.72649 38.411006 169 0 0 32.684927 38.378434 170 0 0 32.63269 38.337724 171 0 0 32.612087 38.319301 172 0 0 32.614007 38.324574 173 0 0 32.633425 38.338704 174 0 0 32.643672 38.341943 175 0 0 32.647722 38.35271 176 0 0 32.660595 38.359214 177 0 0 32.711227 38.402622 178 0 0 32.725314 38.408718 179 0 0 32.754604 38.439156 180 0 0 32.801172 38.479587 181 0 0 32.820053 38.498112 182 0 0 32.897547 38.564321 183 0 0 32.937746 38.592939 184 0 0 32.947677 38.606627 185 0 0 32.999929 38.64921 186 0 0 33.030137 38.669791 187 0 0 33.106995 38.731684 188 0 0 33.079325 38.715509 189 0 0 33.094561 38.7196 190 0 0 33.086804 38.721693 191 0 0 33.111682 38.738801 192 0 0 33.075234 38.725668 193 0 0 33.061018 38.712319 194 0 0 33.057105 38.718466 195 0 0 33.020655 38.697162 196 0 0 33.005023 38.685784 197 0 0 33.018252 38.708823 198 0 0 33.020769 38.705836 199 0 0 33.001116 38.695858 200 0 0 33.01145 38.716607 201 0 0 32.971112 38.691014 202 0 0 32.948501 38.674855 203 0 0 32.953783 38.692398 204 0 0 32.921308 38.671773 205 0 0 32.895954 38.657648 206 0 0 32.885277 38.660894 207 0 0 32.845762 38.62579 208 0 0 32.850001 38.63203 209 0 0 32.882591 38.664761 210 0 0 32.859055 38.647576 211 0 0 32.851968 38.649813 212 0 0 32.838222 38.644452 213 0 0 32.816215 38.63181 214 0 0 32.754898 38.583871 215 0 0 32.762381 38.604766 216 0 0 32.709518 38.572236 217 0 0 32.742008 38.589291 218 0 0 32.65174 38.529165 219 0 0 32.694295 38.564635 220 0 0 32.671543 38.539722 221 0 0 32.60432 38.506171 222 0 0 32.622234 38.517006 223 0 0 32.590398 38.498214 224 0 0 32.659341 38.560821 225 0 0 32.605507 38.512385 226 0 0 32.498645 38.438489 227 0 0 32.553763 38.493398 228 0 0 32.546146 38.471792 229 0 0 32.489227 38.43168 230 0 0 32.452091 38.408849 231 0 0 32.508057 38.458432 232 0 0 32.478547 38.440239 233 0 0 32.394287 38.37991 234 0 0 32.382661 38.370813 235 0 0 32.43726 38.409415 236 0 0 32.373207 38.360707 237 0 0 32.228817 38.26609 238 0 0 32.28814 38.33101 239 0 0 32.244175 38.292418 240 0 0 32.181431 38.248954 241 0 0 32.260838 38.320697 242 0 0 32.233257 38.296683 243 0 0 32.03752 38.157281 244 0 0 32.083345 38.194313 245 0 0 32.001118 38.150296 246 0 0 32.063273 38.19852 247 0 0 31.998061 38.144242 248 0 0 31.83341 38.00689 249 0 0 31.932842 38.109791 250 0 0 32.034275 38.165851 251 0 0 31.870436 38.051153 252 0 0 31.903603 38.105635 253 0 0 31.839385 38.059977 254 0 0 31.836787 38.059163 255 0 0 31.753843 37.998197 256 0 0 31.707129 37.964779 257 0 0 31.60516 37.913061 258 0 0 31.606251 37.89925 259 0 0 31.665608 37.948555 260 0 0 31.387097 37.752507 261 0 0 31.419161 37.770557 262 0 0 31.464962 37.774936 263 0 0 31.5254 37.856029 264 0 0 31.333052 37.734948 265 0 0 31.230408 37.662635 266 0 0 31.194378 37.624816 267 0 0 31.013839 37.475254 268 0 0 31.020527 37.540944 269 0 0 31.181744 37.627696 270 0 0 31.091376 37.583252 271 0 0 30.937385 37.480382 272 0 0 30.778824 37.377945 273 0 0 30.828854 37.402638 274 0 0 30.832377 37.442515 275 0 0 30.686872 37.318179 276 0 0 30.378037 37.053855 277 0 0 30.507333 37.201504 278 0 0 30.35269 37.081867 279 0 0 30.399462 37.126989 280 0 0 30.313597 37.020941 281 0 0 30.121393 36.927164 282 0 0 30.308356 37.02959 283 0 0 30.055443 36.861886 284 0 0 29.797567 36.701134 285 0 0 29.929979 36.740329 286 0 0 29.94645 36.876788 287 0 0 29.788633 36.674065 288 0 0 29.55922 36.536946 289 0 0 29.461828 36.523198 290 0 0 29.516774 36.555913 291 0 0 29.317328 36.386499 292 0 0 29.41464 36.444363 293 0 0 29.399693 36.428742 294 0 0 29.160615 36.252231 295 0 0 29.24021 36.366428 296 0 0 29.309353 36.34801 297 0 0 29.354173 36.397248 298 0 0 29.151496 36.239609 299 0 0 28.708919 35.970162 300 0 0 28.938937 36.119726 301 0 0 28.748378 35.894857 302 0 0 29.018582 36.097333 303 0 0 28.8747 36.108487 304 0 0 28.982671 36.140744 305 0 0 28.54133 35.878407 306 0 0 28.540334 35.835959 307 0 0 28.600204 35.862134 308 0 0 28.396938 35.735192 309 0 0 27.758581 35.200504 310 0 0 28.241228 35.548037 311 0 0 28.131846 35.463602 312 0 0 28.01013 35.434395 313 0 0 28.360592 35.707425 314 0 0 27.986429 35.389313 315 0 0 28.181735 35.525723 316 0 0 28.207243 35.536217 317 0 0 28.435396 35.763301 318 0 0 28.192857 35.484921 319 0 0 28.439791 35.674956 320 0 0 27.768362 35.25 321 0 0 28.160494 35.620885 322 0 0 28.589134 35.814375 323 0 0 28.086466 35.519424 324 0 0 28.474012 35.707554 325 0 0 28.360092 35.634557 326 0 0 27.692308 35.290598 327 0 0 28.355491 35.737958 328 0 0 28.016779 35.551454 329 0 0 27.71161 35.141074 330 0 0 27.958848 35.414266 331 0 0 28.261682 35.548287 332 0 0 27.928962 35.459016 333 0 0 26.248408 34.58811 334 0 0 28.107143 35.559524 335 0 0 27.762295 35.270492 336 0 0 26.302752 34.366972 337 0 0 28.406593 35.919414 338 0 0 28.609756 35.813008 339 0 0 28.944444 36.060185 340 0 0 28.68254 35.582011 341 0 0 29.537037 36.425926 342 0 0 25.666667 33.875 343 0 0 27.333333 34.753968 344 0 0 27.081081 35.207207 345 0 0 27.068966 35.068966 346 0 0 24.964286 33.035714 347 0 0 29.869565 36.347826 348 0 0 30.2 37.033333 349 0 0 27.4375 34.520833 350 0 0 28.2 35.088889 351 0 0 29.214286 35.761905 352 0 0 29.916667 37.027778 353 0 0 27.8 36.3 354 0 0 26.75 34.416667 355 0 0 29.6 35.266667 356 0 0 21.8 31.133333 357 0 0 30.2 36.266667 358 0 0 29.6 37.8 359 0 0 22.75 30.333333 360 0 0 22.25 28.416667 361 0 0 30 36.555556 362 0 0 36 41 363 0 0 17.5 30.666667 364 0 0 15 27 365 0 0 26 31.166667 366 0 0 32 37