## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5286-Z0030-CATGTCTAAGATGAT/441525-L5286-Z0030-CATGTCTAAGATGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5286-Z0030-CATGTCTAAGATGAT/441525-L5286-Z0030-CATGTCTAAGATGAT_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 02:56:57 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 999489 999489 175 175448463 175448463 170644455 170644455 160942609 160942609 0 0 0.972619 0.917321 0 0.972619 0.917321 0 526345389 526345389 520094877 520094877 504827393 504827393 478079421 478079421 0.988125 0.959118 0.9083 0.988125 0.959118 0.9083 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 941 0 35.993411 40.994978 1 13727 0 35.987574 40.991472 2 16822 6253 35.993519 40.994367 3 40228 1692 35.97914 40.982978 4 61638 56480 35.990317 40.992283 5 124511 16897 35.995076 40.995974 6 104271 146895 35.974362 40.980112 7 210663 175707 35.981867 40.987509 8 178143 154774 35.988332 40.990598 9 245412 115051 35.939057 40.948836 10 250077 510431 35.902271 40.935152 11 291807 68701 35.940141 40.957165 12 335514 704549 35.595881 40.662702 13 326897 200786 34.73378 40.218233 14 450727 949270 35.900883 40.9408 15 374106 376544 35.757119 40.833698 16 352062 373732 35.759696 40.790218 17 502496 1020354 35.908982 40.925978 18 541893 716869 35.664721 40.729902 19 382073 655527 35.79146 40.84755 20 570640 940315 35.932778 40.954633 21 672813 1394602 35.846319 40.889469 22 364306 527318 35.641758 40.759367 23 1198377 1432659 35.380821 40.58179 24 609972 1253881 35.436646 40.61888 25 546159 511590 35.414049 40.604491 26 1870180 2661167 35.362749 40.56461 27 378898 983568 35.398664 40.595188 28 971208 441977 35.398339 40.596302 29 2519293 5120407 35.396435 40.592195 30 869261 52438 35.392583 40.591166 31 2557856 1060262 35.395832 40.590772 32 1926951 5355442 35.383679 40.580153 33 971700 158205 35.384482 40.583294 34 2744462 3246217 35.378741 40.579211 35 2538838 3853310 35.396462 40.590072 36 149333541 2636726 35.418631 40.605762 37 0 4346618 35.417488 40.60766 38 0 573077 35.406638 40.600096 39 0 5465677 35.405452 40.599125 40 0 3 35.399257 40.594369 41 0 478079418 35.37913 40.579813 42 0 0 35.373294 40.575717 43 0 0 35.379857 40.579489 44 0 0 35.390178 40.586635 45 0 0 35.392273 40.589592 46 0 0 35.391103 40.587408 47 0 0 35.378353 40.578337 48 0 0 35.370794 40.572584 49 0 0 35.370622 40.572234 50 0 0 35.370725 40.57388 51 0 0 35.372039 40.574766 52 0 0 35.355219 40.563418 53 0 0 35.350686 40.56111 54 0 0 35.358867 40.565654 55 0 0 35.341276 40.553536 56 0 0 35.336551 40.551828 57 0 0 35.341043 40.552684 58 0 0 35.340923 40.553111 59 0 0 35.330825 40.545302 60 0 0 35.321918 40.537757 61 0 0 35.309235 40.528346 62 0 0 35.302585 40.523489 63 0 0 35.28652 40.511727 64 0 0 35.274453 40.503165 65 0 0 35.261173 40.494239 66 0 0 35.254909 40.489775 67 0 0 35.23895 40.47921 68 0 0 35.224408 40.46717 69 0 0 35.211704 40.456909 70 0 0 35.195252 40.444853 71 0 0 35.174454 40.428415 72 0 0 35.154574 40.41339 73 0 0 35.138136 40.400342 74 0 0 35.11451 40.380227 75 0 0 35.091032 40.363034 76 0 0 35.063468 40.340505 77 0 0 35.043063 40.326956 78 0 0 35.022563 40.311306 79 0 0 34.991943 40.286678 80 0 0 34.959151 40.261582 81 0 0 34.929154 40.237076 82 0 0 34.90133 40.214635 83 0 0 34.868058 40.187505 84 0 0 34.845912 40.168579 85 0 0 34.80996 40.141275 86 0 0 34.787413 40.121457 87 0 0 34.766571 40.106421 88 0 0 34.728852 40.077233 89 0 0 34.701435 40.055849 90 0 0 34.67257 40.031038 91 0 0 34.642454 40.004813 92 0 0 34.61317 39.981084 93 0 0 34.588065 39.959371 94 0 0 34.569289 39.943183 95 0 0 34.548083 39.926377 96 0 0 34.525206 39.907361 97 0 0 34.515831 39.899399 98 0 0 34.495631 39.88416 99 0 0 34.480637 39.871136 100 0 0 34.477272 39.86849 101 0 0 34.477947 39.868369 102 0 0 34.473191 39.863689 103 0 0 34.470354 39.86033 104 0 0 34.459794 39.849046 105 0 0 34.457764 39.845761 106 0 0 34.450934 39.839715 107 0 0 34.434093 39.826506 108 0 0 34.410434 39.809755 109 0 0 34.398016 39.800921 110 0 0 34.37463 39.782997 111 0 0 34.336675 39.751549 112 0 0 34.305609 39.722356 113 0 0 34.265425 39.690242 114 0 0 34.222434 39.653948 115 0 0 34.177046 39.61413 116 0 0 34.141485 39.59005 117 0 0 34.107183 39.562476 118 0 0 34.090199 39.551391 119 0 0 34.073833 39.541851 120 0 0 34.064241 39.532672 121 0 0 34.062875 39.53111 122 0 0 34.041486 39.513993 123 0 0 34.024442 39.497212 124 0 0 34.026246 39.498037 125 0 0 34.020763 39.49163 126 0 0 34.019398 39.487095 127 0 0 34.021387 39.485426 128 0 0 34.005348 39.472566 129 0 0 33.991464 39.460794 130 0 0 33.978647 39.451021 131 0 0 33.942866 39.421776 132 0 0 33.939843 39.418131 133 0 0 33.929215 39.408375 134 0 0 33.9169 39.396168 135 0 0 33.896226 39.378174 136 0 0 33.880769 39.36519 137 0 0 33.858559 39.34815 138 0 0 33.857796 39.34756 139 0 0 33.854533 39.34816 140 0 0 33.866115 39.358137 141 0 0 33.879064 39.370051 142 0 0 33.877827 39.369152 143 0 0 33.878001 39.36702 144 0 0 33.859954 39.352112 145 0 0 33.83631 39.329254 146 0 0 33.81025 39.307643 147 0 0 33.771074 39.273268 148 0 0 33.739319 39.245421 149 0 0 33.71039 39.22226 150 0 0 33.66057 39.184461 151 0 0 33.63024 39.162486 152 0 0 33.604293 39.142358 153 0 0 33.577386 39.118816 154 0 0 33.566928 39.112988 155 0 0 33.558314 39.101839 156 0 0 33.548348 39.092402 157 0 0 33.542659 39.087315 158 0 0 33.53505 39.076077 159 0 0 33.54713 39.08894 160 0 0 33.558714 39.100423 161 0 0 33.555294 39.095571 162 0 0 33.579833 39.11409 163 0 0 33.572859 39.108546 164 0 0 33.565579 39.104978 165 0 0 33.54839 39.087087 166 0 0 33.519677 39.061242 167 0 0 33.473571 39.022248 168 0 0 33.420569 38.971322 169 0 0 33.358923 38.918211 170 0 0 33.306327 38.875797 171 0 0 33.259486 38.833599 172 0 0 33.218817 38.803276 173 0 0 33.193894 38.785006 174 0 0 33.186059 38.778423 175 0 0 33.17769 38.776952 176 0 0 33.191751 38.782025 177 0 0 33.219279 38.806983 178 0 0 33.213355 38.801751 179 0 0 33.241111 38.82286 180 0 0 33.272341 38.85077 181 0 0 33.295027 38.870234 182 0 0 33.329047 38.897968 183 0 0 33.366558 38.931981 184 0 0 33.405394 38.961681 185 0 0 33.443565 38.993348 186 0 0 33.463826 39.010977 187 0 0 33.475436 39.021217 188 0 0 33.481367 39.025171 189 0 0 33.499608 39.040989 190 0 0 33.481408 39.027619 191 0 0 33.475753 39.022397 192 0 0 33.451791 39.004738 193 0 0 33.425728 38.9906 194 0 0 33.3844 38.966044 195 0 0 33.384137 38.970591 196 0 0 33.347958 38.948602 197 0 0 33.339115 38.945987 198 0 0 33.322148 38.937435 199 0 0 33.32462 38.944285 200 0 0 33.300946 38.936611 201 0 0 33.287799 38.934212 202 0 0 33.269204 38.924848 203 0 0 33.252679 38.918339 204 0 0 33.230474 38.912873 205 0 0 33.20558 38.899126 206 0 0 33.172115 38.881002 207 0 0 33.139995 38.862315 208 0 0 33.130907 38.860456 209 0 0 33.107657 38.846787 210 0 0 33.080422 38.832132 211 0 0 33.067628 38.827056 212 0 0 33.041768 38.810795 213 0 0 33.032732 38.808873 214 0 0 32.991054 38.780227 215 0 0 32.972886 38.773012 216 0 0 32.949683 38.755477 217 0 0 32.929184 38.74711 218 0 0 32.936414 38.753058 219 0 0 32.906654 38.740434 220 0 0 32.902121 38.730493 221 0 0 32.875094 38.714399 222 0 0 32.834411 38.691722 223 0 0 32.814186 38.678185 224 0 0 32.785148 38.657685 225 0 0 32.773497 38.653576 226 0 0 32.755036 38.640157 227 0 0 32.741233 38.635397 228 0 0 32.726957 38.619769 229 0 0 32.681794 38.595964 230 0 0 32.656303 38.584609 231 0 0 32.66322 38.588648 232 0 0 32.599222 38.547312 233 0 0 32.553433 38.517353 234 0 0 32.562161 38.525672 235 0 0 32.479797 38.462168 236 0 0 32.470948 38.468958 237 0 0 32.446884 38.449628 238 0 0 32.438365 38.4494 239 0 0 32.410596 38.428522 240 0 0 32.37809 38.412502 241 0 0 32.326608 38.369963 242 0 0 32.329668 38.376353 243 0 0 32.319393 38.376547 244 0 0 32.214192 38.301013 245 0 0 32.210438 38.299296 246 0 0 32.205288 38.296734 247 0 0 32.175187 38.27983 248 0 0 32.138927 38.26698 249 0 0 32.164909 38.282084 250 0 0 32.051272 38.21055 251 0 0 32.024097 38.191174 252 0 0 32.043594 38.191774 253 0 0 31.999331 38.173516 254 0 0 31.958759 38.14841 255 0 0 31.920868 38.129641 256 0 0 31.866752 38.084848 257 0 0 31.86342 38.087715 258 0 0 31.835759 38.066558 259 0 0 31.799804 38.055763 260 0 0 31.701112 37.990113 261 0 0 31.742206 38.012884 262 0 0 31.656104 37.961441 263 0 0 31.668927 37.973037 264 0 0 31.569533 37.901593 265 0 0 31.5187 37.873058 266 0 0 31.430521 37.805573 267 0 0 31.380071 37.764052 268 0 0 31.323867 37.756554 269 0 0 31.401681 37.785431 270 0 0 31.235074 37.694609 271 0 0 31.116394 37.605812 272 0 0 31.097138 37.60443 273 0 0 31.043177 37.544874 274 0 0 31.007414 37.53468 275 0 0 30.929815 37.486184 276 0 0 30.849703 37.427175 277 0 0 30.855785 37.436057 278 0 0 30.819809 37.410811 279 0 0 30.68297 37.305636 280 0 0 30.616615 37.280092 281 0 0 30.552357 37.227361 282 0 0 30.438798 37.13781 283 0 0 30.411531 37.141188 284 0 0 30.39958 37.132473 285 0 0 30.284889 37.057947 286 0 0 30.252309 37.02649 287 0 0 30.175119 36.988589 288 0 0 30.102605 36.92996 289 0 0 30.043309 36.880619 290 0 0 29.974478 36.839913 291 0 0 29.941432 36.789123 292 0 0 29.750903 36.685753 293 0 0 29.741472 36.677851 294 0 0 29.5983 36.570976 295 0 0 29.680609 36.629412 296 0 0 29.547999 36.527513 297 0 0 29.468689 36.495128 298 0 0 29.484855 36.514457 299 0 0 29.424485 36.439621 300 0 0 29.425754 36.431117 301 0 0 29.335037 36.387608 302 0 0 29.301087 36.36775 303 0 0 29.081778 36.214143 304 0 0 29.164787 36.290093 305 0 0 29.079824 36.189922 306 0 0 29.123565 36.246364 307 0 0 29.094435 36.186486 308 0 0 29.038302 36.146258 309 0 0 28.796731 35.97581 310 0 0 28.907241 36.067848 311 0 0 28.760518 35.964857 312 0 0 28.80838 36.001966 313 0 0 28.638272 35.867448 314 0 0 28.660249 35.899247 315 0 0 28.738777 35.92617 316 0 0 28.706621 35.914683 317 0 0 28.723268 35.952918 318 0 0 28.883227 36.053504 319 0 0 28.542584 35.84181 320 0 0 28.538016 35.796532 321 0 0 28.500721 35.804554 322 0 0 28.620778 35.860557 323 0 0 28.439147 35.725234 324 0 0 28.096681 35.479798 325 0 0 28.236393 35.600409 326 0 0 28.249192 35.510922 327 0 0 28.281179 35.594536 328 0 0 28.196262 35.520129 329 0 0 28.245192 35.66039 330 0 0 28.261144 35.578418 331 0 0 28.278856 35.616105 332 0 0 28.189528 35.519256 333 0 0 27.592853 35.082748 334 0 0 28.158423 35.565591 335 0 0 27.702128 35.227769 336 0 0 28.249765 35.549296 337 0 0 27.907466 35.373992 338 0 0 28.688466 35.889417 339 0 0 27.627717 35.158514 340 0 0 28.484985 35.87037 341 0 0 27.392123 35.035959 342 0 0 27.772816 35.133981 343 0 0 27.364653 35.13572 344 0 0 27.728205 35.429915 345 0 0 27.810345 35.153257 346 0 0 27.851485 35.39604 347 0 0 28.284091 35.680556 348 0 0 27.565789 35.247076 349 0 0 27.602041 35.333333 350 0 0 28.022727 35.214015 351 0 0 29.088608 36.080169 352 0 0 27.778626 35.086514 353 0 0 28.090909 35.763636 354 0 0 27.646465 35.087542 355 0 0 27.188889 34.833333 356 0 0 28.012987 35.160173 357 0 0 26.041667 34.361111 358 0 0 28.84127 36.206349 359 0 0 28.529412 36.143791 360 0 0 28.102041 35.605442 361 0 0 26.641026 34.068376 362 0 0 30.277778 37.277778 363 0 0 29.323529 36.039216 364 0 0 27.424242 34.808081 365 0 0 29.7 36.833333 366 0 0 27.241379 34.264368 367 0 0 25.875 33.25 368 0 0 28.95 36.383333 369 0 0 28.941176 34.941176 370 0 0 21.066667 30.022222 371 0 0 30 36.820513 372 0 0 29.5 36.888889 373 0 0 31.636364 38.212121 374 0 0 29.636364 36.333333 375 0 0 29.727273 37.151515 376 0 0 24.454545 32.848485 377 0 0 27.75 35.416667 378 0 0 20.714286 30.285714 379 0 0 27.333333 35.222222 380 0 0 25 34.8 381 0 0 22.666667 33.444444 382 0 0 28.666667 38 383 0 0 34.333333 39.444444 384 0 0 34.666667 40 385 0 0 28.666667 37.111111 386 0 0 24.5 36.333333 387 0 0 27 36.333333 388 0 0 36 41 389 0 0 29 37 390 0 0 36 41 391 0 0 29 37 392 0 0 36 41 393 0 0 34 39.333333 394 0 0 36 41 395 0 0 18 28.333333 396 0 0 36 41 397 0 0 36 41