## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5274-Z0013-CAGTTGTGCTGTGAT/441525-L5274-Z0013-CAGTTGTGCTGTGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5274-Z0013-CAGTTGTGCTGTGAT/441525-L5274-Z0013-CAGTTGTGCTGTGAT_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 03:00:03 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 997484 997484 149 149011195 149011195 144385770 144385770 135123464 135123464 0 0 0.968959 0.906801 0 0.968959 0.906801 0 447033585 447033585 440974284 440974284 426352249 426352249 401059118 401059118 0.986446 0.953737 0.897157 0.986446 0.953737 0.897157 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 751 0 35.992941 40.994515 1 10066 0 35.985036 40.989643 2 12434 4382 35.99442 40.995171 3 30858 1230 35.981015 40.98464 4 50582 42290 35.989633 40.991534 5 99993 14682 35.99395 40.995139 6 99755 111167 35.973512 40.978264 7 176622 140655 35.979585 40.985687 8 176954 135536 35.987749 40.990092 9 221068 93907 35.945393 40.953883 10 230443 470001 35.896599 40.931972 11 274881 53968 35.941282 40.957645 12 330156 661305 35.269456 40.390073 13 335641 188243 33.87178 39.683929 14 434851 939315 35.884829 40.929193 15 350231 349000 35.806097 40.86162 16 371661 409903 35.730266 40.758609 17 505154 1070967 35.890271 40.905818 18 536883 675309 35.731508 40.783287 19 376441 697441 35.797886 40.852508 20 510317 994917 35.932019 40.95418 21 645265 1323423 35.850771 40.893198 22 332864 565075 35.664626 40.774125 23 1048645 1223591 35.430582 40.622616 24 582188 1166911 35.464264 40.639935 25 544135 497580 35.446136 40.627496 26 1796230 2501709 35.412617 40.602823 27 358676 894119 35.426496 40.612555 28 961021 389120 35.441644 40.622835 29 2482965 5065590 35.436206 40.618876 30 791559 44078 35.422177 40.60737 31 2403362 870596 35.424059 40.609252 32 1670151 5408882 35.419815 40.606186 33 870488 125786 35.41982 40.605668 34 2538926 2750056 35.406445 40.598623 35 2362759 3899539 35.428693 40.612388 36 124486219 2154353 35.440421 40.620864 37 0 4379160 35.444829 40.625305 38 0 441332 35.43305 40.616827 39 0 5219349 35.43705 40.619698 40 0 1 35.430773 40.61399 41 0 401059117 35.424806 40.611852 42 0 0 35.415907 40.604056 43 0 0 35.420877 40.606866 44 0 0 35.432485 40.614504 45 0 0 35.427933 40.611061 46 0 0 35.428879 40.612838 47 0 0 35.421773 40.607065 48 0 0 35.41762 40.603637 49 0 0 35.410922 40.600345 50 0 0 35.408977 40.59829 51 0 0 35.402144 40.593091 52 0 0 35.401113 40.592741 53 0 0 35.39632 40.58864 54 0 0 35.390953 40.585722 55 0 0 35.388144 40.583711 56 0 0 35.376367 40.576406 57 0 0 35.368672 40.570848 58 0 0 35.355809 40.560105 59 0 0 35.336248 40.546359 60 0 0 35.317166 40.532463 61 0 0 35.290984 40.513739 62 0 0 35.268215 40.495739 63 0 0 35.238664 40.473097 64 0 0 35.205743 40.44797 65 0 0 35.168421 40.420019 66 0 0 35.126258 40.388806 67 0 0 35.071223 40.349442 68 0 0 35.019036 40.311422 69 0 0 34.955631 40.261767 70 0 0 34.891238 40.212165 71 0 0 34.813026 40.150132 72 0 0 34.748646 40.095663 73 0 0 34.671381 40.035127 74 0 0 34.586351 39.970395 75 0 0 34.516556 39.917845 76 0 0 34.433575 39.853755 77 0 0 34.365261 39.803111 78 0 0 34.29924 39.751462 79 0 0 34.230865 39.698316 80 0 0 34.162504 39.643622 81 0 0 34.111065 39.601532 82 0 0 34.051039 39.554609 83 0 0 34.009892 39.517371 84 0 0 33.961487 39.480561 85 0 0 33.930306 39.456551 86 0 0 33.889172 39.424884 87 0 0 33.850486 39.391525 88 0 0 33.814093 39.361272 89 0 0 33.771273 39.324764 90 0 0 33.721441 39.283905 91 0 0 33.689227 39.254863 92 0 0 33.645708 39.218616 93 0 0 33.615621 39.190651 94 0 0 33.578803 39.161961 95 0 0 33.561478 39.145579 96 0 0 33.525713 39.115433 97 0 0 33.509547 39.10402 98 0 0 33.50358 39.096003 99 0 0 33.506162 39.098614 100 0 0 33.524019 39.113069 101 0 0 33.546558 39.129795 102 0 0 33.567512 39.143156 103 0 0 33.585316 39.156068 104 0 0 33.591977 39.158286 105 0 0 33.614105 39.174419 106 0 0 33.617741 39.172737 107 0 0 33.610901 39.165589 108 0 0 33.605025 39.164227 109 0 0 33.585495 39.146755 110 0 0 33.570313 39.134458 111 0 0 33.529734 39.103543 112 0 0 33.489277 39.068579 113 0 0 33.436623 39.025559 114 0 0 33.387262 38.982778 115 0 0 33.328956 38.937 116 0 0 33.30443 38.918461 117 0 0 33.283687 38.904197 118 0 0 33.277974 38.90133 119 0 0 33.267229 38.894111 120 0 0 33.272368 38.899597 121 0 0 33.258756 38.887321 122 0 0 33.268273 38.894402 123 0 0 33.267301 38.889728 124 0 0 33.258325 38.882226 125 0 0 33.270235 38.888221 126 0 0 33.285886 38.899743 127 0 0 33.278164 38.882504 128 0 0 33.250048 38.862764 129 0 0 33.228996 38.845619 130 0 0 33.196807 38.81833 131 0 0 33.183493 38.805294 132 0 0 33.168886 38.793607 133 0 0 33.150958 38.777825 134 0 0 33.153665 38.776553 135 0 0 33.152512 38.775526 136 0 0 33.127364 38.755227 137 0 0 33.112124 38.743219 138 0 0 33.108299 38.73751 139 0 0 33.111273 38.74622 140 0 0 33.135445 38.763762 141 0 0 33.156031 38.779256 142 0 0 33.171063 38.791357 143 0 0 33.162792 38.783584 144 0 0 33.140431 38.763892 145 0 0 33.133335 38.756651 146 0 0 33.11157 38.733265 147 0 0 33.064306 38.692917 148 0 0 33.041994 38.673652 149 0 0 33.004155 38.645555 150 0 0 32.963732 38.615684 151 0 0 32.953055 38.600161 152 0 0 32.926823 38.583954 153 0 0 32.917862 38.575691 154 0 0 32.912176 38.570933 155 0 0 32.911278 38.569275 156 0 0 32.93189 38.585557 157 0 0 32.953402 38.601643 158 0 0 32.967285 38.610522 159 0 0 33.013266 38.648532 160 0 0 33.011927 38.65108 161 0 0 33.060748 38.683228 162 0 0 33.07418 38.697428 163 0 0 33.092967 38.709493 164 0 0 33.097271 38.715079 165 0 0 33.116284 38.729784 166 0 0 33.089161 38.703593 167 0 0 33.085514 38.698797 168 0 0 33.061121 38.671109 169 0 0 33.016523 38.635398 170 0 0 32.993838 38.618644 171 0 0 32.967054 38.599543 172 0 0 32.954886 38.586329 173 0 0 32.977453 38.607844 174 0 0 32.986537 38.615457 175 0 0 33.004588 38.63396 176 0 0 33.033771 38.655178 177 0 0 33.060764 38.68379 178 0 0 33.104456 38.716884 179 0 0 33.148256 38.751872 180 0 0 33.173436 38.773651 181 0 0 33.221953 38.819752 182 0 0 33.27284 38.86107 183 0 0 33.283277 38.871741 184 0 0 33.324875 38.904544 185 0 0 33.329346 38.907982 186 0 0 33.369178 38.944056 187 0 0 33.420828 38.984302 188 0 0 33.430838 38.991053 189 0 0 33.420878 38.98927 190 0 0 33.433715 38.99879 191 0 0 33.409338 38.979658 192 0 0 33.383324 38.969819 193 0 0 33.389726 38.975071 194 0 0 33.36665 38.964907 195 0 0 33.354003 38.960352 196 0 0 33.375501 38.983274 197 0 0 33.374656 38.98679 198 0 0 33.360879 38.983126 199 0 0 33.353852 38.982245 200 0 0 33.351095 38.987554 201 0 0 33.329305 38.976891 202 0 0 33.303617 38.961611 203 0 0 33.303337 38.975666 204 0 0 33.28297 38.964347 205 0 0 33.252376 38.942544 206 0 0 33.260961 38.956894 207 0 0 33.249092 38.95045 208 0 0 33.222811 38.932138 209 0 0 33.204493 38.929065 210 0 0 33.194382 38.918926 211 0 0 33.191915 38.922798 212 0 0 33.190395 38.924967 213 0 0 33.162612 38.908529 214 0 0 33.12513 38.881984 215 0 0 33.115901 38.873958 216 0 0 33.098215 38.86588 217 0 0 33.070543 38.844339 218 0 0 33.031515 38.822975 219 0 0 33.066333 38.855274 220 0 0 33.032961 38.825412 221 0 0 32.996858 38.808397 222 0 0 32.97914 38.796804 223 0 0 32.952576 38.786141 224 0 0 32.942529 38.776924 225 0 0 32.920157 38.757915 226 0 0 32.925105 38.763571 227 0 0 32.848026 38.712195 228 0 0 32.771097 38.658487 229 0 0 32.782587 38.674827 230 0 0 32.780713 38.676439 231 0 0 32.760512 38.666463 232 0 0 32.775699 38.678049 233 0 0 32.7254 38.64929 234 0 0 32.720929 38.635104 235 0 0 32.676055 38.610914 236 0 0 32.669795 38.613193 237 0 0 32.610365 38.564357 238 0 0 32.651013 38.605021 239 0 0 32.622351 38.576206 240 0 0 32.580627 38.562969 241 0 0 32.560177 38.541747 242 0 0 32.536197 38.534877 243 0 0 32.483074 38.486896 244 0 0 32.498724 38.50394 245 0 0 32.413929 38.449189 246 0 0 32.423362 38.454097 247 0 0 32.377434 38.42824 248 0 0 32.316728 38.400823 249 0 0 32.320251 38.383135 250 0 0 32.238897 38.332205 251 0 0 32.205477 38.324041 252 0 0 32.13667 38.276296 253 0 0 32.220446 38.331066 254 0 0 32.133694 38.270888 255 0 0 32.138952 38.281103 256 0 0 32.109038 38.257861 257 0 0 32.007293 38.19645 258 0 0 32.031179 38.220556 259 0 0 31.960074 38.162107 260 0 0 31.93023 38.128642 261 0 0 31.805258 38.060442 262 0 0 31.794197 38.04197 263 0 0 31.795189 38.050779 264 0 0 31.692856 38.002501 265 0 0 31.594084 37.919942 266 0 0 31.577896 37.888908 267 0 0 31.568348 37.926381 268 0 0 31.477889 37.830852 269 0 0 31.370136 37.761439 270 0 0 31.328484 37.747792 271 0 0 31.328608 37.739486 272 0 0 31.221063 37.669424 273 0 0 31.231499 37.696826 274 0 0 31.138619 37.618519 275 0 0 31.170943 37.625103 276 0 0 31.050445 37.582437 277 0 0 31.047724 37.578902 278 0 0 30.912459 37.476068 279 0 0 30.77013 37.391417 280 0 0 30.645511 37.294789 281 0 0 30.735271 37.340199 282 0 0 30.56588 37.240832 283 0 0 30.423773 37.145055 284 0 0 30.508806 37.212392 285 0 0 30.37348 37.110744 286 0 0 30.318534 37.066588 287 0 0 30.263185 37.02779 288 0 0 30.120523 36.946463 289 0 0 30.028262 36.84778 290 0 0 30.026206 36.865825 291 0 0 29.922551 36.811424 292 0 0 29.862981 36.736409 293 0 0 29.742213 36.666264 294 0 0 29.680982 36.630969 295 0 0 29.551396 36.512936 296 0 0 29.619036 36.594678 297 0 0 29.677891 36.625548 298 0 0 29.575564 36.551698 299 0 0 29.185223 36.259013 300 0 0 29.325733 36.397545 301 0 0 29.202253 36.297916 302 0 0 29.218114 36.269527 303 0 0 29.220658 36.295135 304 0 0 29.222196 36.308528 305 0 0 29.004645 36.158313 306 0 0 28.896356 36.06416 307 0 0 29.010773 36.151916 308 0 0 28.980006 36.1218 309 0 0 28.799349 35.999897 310 0 0 28.751766 35.954877 311 0 0 28.790501 35.969452 312 0 0 28.905319 36.063435 313 0 0 28.40818 35.720726 314 0 0 28.503486 35.719971 315 0 0 28.641218 35.85324 316 0 0 28.7091 35.912577 317 0 0 28.598222 35.84116 318 0 0 28.431995 35.731776 319 0 0 28.288882 35.576024 320 0 0 28.638563 35.955176 321 0 0 28.290348 35.614302 322 0 0 28.372023 35.631009 323 0 0 28.139344 35.511411 324 0 0 28.229751 35.557614 325 0 0 28.308542 35.672671 326 0 0 28.54042 35.769361 327 0 0 28.076204 35.586868 328 0 0 27.958098 35.420629 329 0 0 28.19306 35.577995 330 0 0 28.383698 35.604705 331 0 0 27.908886 35.332583 332 0 0 27.978616 35.51153 333 0 0 28.200843 35.555712 334 0 0 28.670492 35.818033 335 0 0 27.856322 35.49553 336 0 0 28.272727 35.681818 337 0 0 26.997512 34.812604 338 0 0 28.056757 35.377477 339 0 0 27.89441 35.454451 340 0 0 27.391608 35.030303 341 0 0 27.330645 35.169355 342 0 0 27.497696 35.158218 343 0 0 27.834171 35.489112 344 0 0 27.447059 34.929412 345 0 0 27.310345 35.464368 346 0 0 27.992248 35.490956 347 0 0 27.899083 35.666667 348 0 0 27.113402 35.381443 349 0 0 28.8 35.996078 350 0 0 24.942857 33.566667 351 0 0 28.25 36.109375 352 0 0 28.037037 35.734568 353 0 0 27.647059 35.326797 354 0 0 27.914894 35.177305 355 0 0 29.880952 36.666667 356 0 0 28.777778 36.222222 357 0 0 26.583333 34.925926 358 0 0 27.264706 34.784314 359 0 0 26.875 34.916667 360 0 0 24.37931 33.747126 361 0 0 25.846154 33.525641 362 0 0 29.619048 36.31746 363 0 0 29.473684 36.403509 364 0 0 28.1875 35.354167 365 0 0 28.533333 35.444444 366 0 0 24 32.809524 367 0 0 27.142857 34.333333 368 0 0 29.5 35.444444 369 0 0 26 33.083333 370 0 0 32.636364 39.212121 371 0 0 28.5 34.7 372 0 0 29.555556 36.814815 373 0 0 25.833333 32 374 0 0 27.6 33.533333 375 0 0 36 41 376 0 0 36 41 377 0 0 36 41 378 0 0 27 34.333333 379 0 0 36 41 380 0 0 31 38 381 0 0 23 35 382 0 0 20 29