## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5411-Z0103-CATATAATCACAGAT/441525-L5411-Z0103-CATATAATCACAGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5411-Z0103-CATATAATCACAGAT/441525-L5411-Z0103-CATATAATCACAGAT_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 1001884 1001884 139 139332855 139332855 134258314 134258314 124963874 124963874 0 0 0.96358 0.896873 0 0.96358 0.896873 0 417998565 417998565 411310594 411310594 396337662 396337662 371301402 371301402 0.984 0.948179 0.888284 0.984 0.948179 0.888284 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 956 1 35.993563 40.995244 1 12574 0 35.987656 40.991559 2 14735 4997 35.994564 40.99556 3 37519 1448 35.984096 40.987002 4 58728 53409 35.992007 40.993484 5 118896 19152 35.995279 40.996166 6 109401 136564 35.979962 40.983734 7 205997 170504 35.979851 40.986165 8 193116 150980 35.987622 40.989766 9 252346 119867 35.954246 40.961145 10 265202 509622 35.907674 40.939358 11 312867 67671 35.946477 40.961412 12 369764 728651 35.340442 40.442816 13 360977 222076 33.9664 39.743037 14 484813 1034207 35.905011 40.943136 15 386251 391048 35.799211 40.856924 16 403249 448030 35.778223 40.800659 17 532232 1147295 35.903393 40.919097 18 573841 755982 35.761876 40.804682 19 381077 726467 35.773078 40.8381 20 531978 1017739 35.914892 40.945074 21 673164 1416891 35.845424 40.887856 22 334144 567854 35.620662 40.736111 23 1071046 1250561 35.31243 40.526115 24 593280 1245945 35.314213 40.532107 25 536682 479898 35.307436 40.528332 26 1777183 2582969 35.242503 40.481051 27 373249 908249 35.251463 40.491351 28 952054 395541 35.270343 40.505873 29 2451660 5107285 35.263432 40.498753 30 776854 43008 35.254243 40.492436 31 2349490 855905 35.251391 40.488788 32 1680460 5456869 35.240867 40.479769 33 870474 131854 35.238014 40.479553 34 2481825 2768235 35.234329 40.477212 35 2241017 3850783 35.244814 40.484016 36 114563754 2225307 35.270185 40.500924 37 0 4249104 35.267704 40.5005 38 0 419999 35.255218 40.493979 39 0 5035196 35.258837 40.494337 40 0 1 35.245465 40.484801 41 0 371301401 35.232116 40.474689 42 0 0 35.22356 40.467921 43 0 0 35.223786 40.468096 44 0 0 35.236785 40.476687 45 0 0 35.238704 40.478515 46 0 0 35.234042 40.475062 47 0 0 35.22464 40.469169 48 0 0 35.215786 40.461797 49 0 0 35.206717 40.454524 50 0 0 35.206537 40.456068 51 0 0 35.196667 40.450226 52 0 0 35.182251 40.439423 53 0 0 35.156527 40.421356 54 0 0 35.160016 40.42168 55 0 0 35.137363 40.405784 56 0 0 35.119104 40.392178 57 0 0 35.108378 40.385186 58 0 0 35.081754 40.365288 59 0 0 35.053213 40.343754 60 0 0 35.01423 40.319741 61 0 0 34.975457 40.290445 62 0 0 34.935533 40.25826 63 0 0 34.892594 40.224617 64 0 0 34.836231 40.181849 65 0 0 34.776474 40.138067 66 0 0 34.723951 40.098675 67 0 0 34.644833 40.040834 68 0 0 34.571959 39.986231 69 0 0 34.493015 39.926484 70 0 0 34.407228 39.860158 71 0 0 34.307026 39.778652 72 0 0 34.203389 39.69799 73 0 0 34.107846 39.619813 74 0 0 34.006646 39.542437 75 0 0 33.905609 39.46118 76 0 0 33.806747 39.387061 77 0 0 33.713977 39.315426 78 0 0 33.637621 39.255879 79 0 0 33.550434 39.186501 80 0 0 33.482911 39.134214 81 0 0 33.421465 39.082817 82 0 0 33.371834 39.044496 83 0 0 33.33864 39.012745 84 0 0 33.296941 38.980467 85 0 0 33.264301 38.951929 86 0 0 33.249254 38.939445 87 0 0 33.209743 38.904476 88 0 0 33.184416 38.880113 89 0 0 33.157264 38.856456 90 0 0 33.113444 38.819925 91 0 0 33.083727 38.793324 92 0 0 33.051476 38.761351 93 0 0 33.023391 38.735797 94 0 0 32.978175 38.70115 95 0 0 32.962143 38.683703 96 0 0 32.936775 38.663626 97 0 0 32.913598 38.645349 98 0 0 32.90519 38.639388 99 0 0 32.913051 38.642842 100 0 0 32.934477 38.664518 101 0 0 32.978237 38.696129 102 0 0 33.006068 38.715966 103 0 0 33.053829 38.750786 104 0 0 33.084583 38.773195 105 0 0 33.124389 38.801342 106 0 0 33.140441 38.811952 107 0 0 33.161396 38.825911 108 0 0 33.170209 38.832539 109 0 0 33.153551 38.821901 110 0 0 33.147531 38.816917 111 0 0 33.131751 38.801257 112 0 0 33.084094 38.762408 113 0 0 33.047715 38.73288 114 0 0 32.987238 38.679666 115 0 0 32.952555 38.653431 116 0 0 32.917935 38.62841 117 0 0 32.887216 38.603244 118 0 0 32.877524 38.598584 119 0 0 32.886648 38.612532 120 0 0 32.906757 38.62882 121 0 0 32.942547 38.656517 122 0 0 32.962468 38.669266 123 0 0 32.976212 38.676427 124 0 0 32.993808 38.688359 125 0 0 33.026872 38.71113 126 0 0 33.043964 38.719527 127 0 0 33.063438 38.732543 128 0 0 33.064562 38.730278 129 0 0 33.0462 38.714041 130 0 0 33.036105 38.705904 131 0 0 33.013306 38.688364 132 0 0 33.015385 38.685656 133 0 0 33.00463 38.672493 134 0 0 32.992421 38.664068 135 0 0 32.997059 38.665854 136 0 0 32.976671 38.648975 137 0 0 32.968217 38.640509 138 0 0 32.959152 38.638044 139 0 0 32.976507 38.650574 140 0 0 32.997002 38.671472 141 0 0 33.031755 38.700389 142 0 0 33.056054 38.7177 143 0 0 33.051918 38.715406 144 0 0 33.051456 38.70964 145 0 0 33.045297 38.701069 146 0 0 33.023339 38.680893 147 0 0 32.999533 38.65554 148 0 0 32.964837 38.623428 149 0 0 32.912789 38.5861 150 0 0 32.876564 38.554212 151 0 0 32.852749 38.541273 152 0 0 32.830554 38.523699 153 0 0 32.810624 38.51125 154 0 0 32.815431 38.510145 155 0 0 32.81042 38.508831 156 0 0 32.816738 38.507163 157 0 0 32.82643 38.511009 158 0 0 32.85292 38.534769 159 0 0 32.880409 38.552531 160 0 0 32.901007 38.572591 161 0 0 32.939078 38.596551 162 0 0 32.960209 38.612312 163 0 0 32.965058 38.617653 164 0 0 32.985661 38.634995 165 0 0 32.974285 38.626241 166 0 0 32.944444 38.595471 167 0 0 32.935434 38.579716 168 0 0 32.86687 38.522005 169 0 0 32.798434 38.464564 170 0 0 32.756388 38.428834 171 0 0 32.715151 38.394176 172 0 0 32.678344 38.363087 173 0 0 32.68258 38.367571 174 0 0 32.677016 38.368736 175 0 0 32.679993 38.367638 176 0 0 32.709471 38.394332 177 0 0 32.744737 38.421986 178 0 0 32.752682 38.428461 179 0 0 32.826343 38.488835 180 0 0 32.853815 38.513828 181 0 0 32.913361 38.560383 182 0 0 32.959303 38.605788 183 0 0 33.011854 38.643435 184 0 0 33.037732 38.667928 185 0 0 33.088596 38.707833 186 0 0 33.122338 38.73557 187 0 0 33.158883 38.76519 188 0 0 33.196046 38.794391 189 0 0 33.165058 38.771838 190 0 0 33.210115 38.813309 191 0 0 33.206593 38.804291 192 0 0 33.127511 38.750862 193 0 0 33.112359 38.739595 194 0 0 33.07452 38.719947 195 0 0 33.039062 38.697761 196 0 0 33.018151 38.692093 197 0 0 33.00597 38.686252 198 0 0 33.005244 38.690912 199 0 0 32.985562 38.690839 200 0 0 32.974641 38.687064 201 0 0 32.968768 38.690357 202 0 0 32.960616 38.686078 203 0 0 32.917537 38.670746 204 0 0 32.911465 38.673527 205 0 0 32.861018 38.642844 206 0 0 32.881458 38.659826 207 0 0 32.873694 38.669522 208 0 0 32.845358 38.650472 209 0 0 32.823009 38.638814 210 0 0 32.778988 38.607192 211 0 0 32.762358 38.595325 212 0 0 32.732533 38.580383 213 0 0 32.694316 38.553236 214 0 0 32.70162 38.567093 215 0 0 32.71473 38.580401 216 0 0 32.645399 38.53222 217 0 0 32.677228 38.558018 218 0 0 32.621524 38.518954 219 0 0 32.598396 38.50067 220 0 0 32.590882 38.495264 221 0 0 32.609826 38.513144 222 0 0 32.525431 38.45194 223 0 0 32.545261 38.481186 224 0 0 32.56779 38.490401 225 0 0 32.50489 38.452438 226 0 0 32.4989 38.449595 227 0 0 32.496033 38.450182 228 0 0 32.446614 38.423429 229 0 0 32.440356 38.414797 230 0 0 32.33765 38.340176 231 0 0 32.424638 38.408482 232 0 0 32.398097 38.383526 233 0 0 32.337824 38.354063 234 0 0 32.402881 38.404177 235 0 0 32.318284 38.347978 236 0 0 32.346035 38.354652 237 0 0 32.276647 38.318843 238 0 0 32.244965 38.285739 239 0 0 32.292886 38.33708 240 0 0 32.21336 38.273102 241 0 0 32.202959 38.276829 242 0 0 32.180037 38.267304 243 0 0 32.147439 38.230906 244 0 0 32.109085 38.225118 245 0 0 32.093384 38.19088 246 0 0 32.108194 38.215384 247 0 0 32.165765 38.25743 248 0 0 32.093195 38.22872 249 0 0 31.941443 38.103081 250 0 0 32.091924 38.203735 251 0 0 32.009516 38.142739 252 0 0 32.014914 38.165809 253 0 0 31.924735 38.119255 254 0 0 31.889279 38.101266 255 0 0 31.830795 38.06878 256 0 0 31.86506 38.095943 257 0 0 31.761572 37.993513 258 0 0 31.760974 37.989811 259 0 0 31.747965 38.02984 260 0 0 31.737697 38.00279 261 0 0 31.617036 37.912096 262 0 0 31.600269 37.890133 263 0 0 31.49723 37.830625 264 0 0 31.485909 37.835036 265 0 0 31.35016 37.745915 266 0 0 31.478941 37.842776 267 0 0 31.377351 37.791905 268 0 0 31.397369 37.793485 269 0 0 31.397221 37.818422 270 0 0 31.220675 37.674669 271 0 0 31.153691 37.640117 272 0 0 31.035951 37.547935 273 0 0 30.961341 37.512497 274 0 0 30.959971 37.521841 275 0 0 30.811249 37.416179 276 0 0 30.808047 37.402217 277 0 0 30.728002 37.32964 278 0 0 30.704835 37.337103 279 0 0 30.703866 37.316284 280 0 0 30.518725 37.176481 281 0 0 30.592413 37.316258 282 0 0 30.510253 37.214633 283 0 0 30.401472 37.120206 284 0 0 30.185256 36.992318 285 0 0 30.008006 36.834592 286 0 0 30.175989 36.99248 287 0 0 30.148148 36.970063 288 0 0 29.945906 36.795337 289 0 0 29.866566 36.755174 290 0 0 29.871826 36.789543 291 0 0 29.673382 36.599453 292 0 0 29.651551 36.615691 293 0 0 29.441667 36.459722 294 0 0 29.439077 36.475552 295 0 0 29.262889 36.269026 296 0 0 29.495425 36.471164 297 0 0 29.367089 36.384484 298 0 0 29.272874 36.322271 299 0 0 29.199903 36.33116 300 0 0 29.309155 36.38693 301 0 0 29.124801 36.19977 302 0 0 29.071866 36.181151 303 0 0 29.009437 36.14568 304 0 0 29.094779 36.239072 305 0 0 28.948214 36.16104 306 0 0 28.941994 36.137085 307 0 0 29.049498 36.147997 308 0 0 28.786164 36.007993 309 0 0 29.174131 36.281568 310 0 0 28.877798 36.049687 311 0 0 29.135683 36.234186 312 0 0 28.475869 35.786369 313 0 0 28.516835 35.8685 314 0 0 28.485472 35.819814 315 0 0 28.593812 35.861532 316 0 0 28.978525 36.141971 317 0 0 28.657054 35.873993 318 0 0 28.267902 35.506038 319 0 0 28.434822 35.615314 320 0 0 28.599606 35.838922 321 0 0 28.340885 35.687882 322 0 0 28.22924 35.545029 323 0 0 28.498711 35.841924 324 0 0 28.292135 35.61985 325 0 0 28.253543 35.609974 326 0 0 27.857143 35.373494 327 0 0 27.640832 35.033396 328 0 0 27.858051 35.272599 329 0 0 27.659574 35.208826 330 0 0 28.00271 35.344173 331 0 0 29.059172 35.965483 332 0 0 28.160959 35.547945 333 0 0 28.29771 35.475827 334 0 0 28.354701 35.878917 335 0 0 27.395 35.121667 336 0 0 29.011429 36.470476 337 0 0 29.478261 36.482402 338 0 0 27.226027 35.009132 339 0 0 28.135338 35.080201 340 0 0 28.491379 35.882184 341 0 0 27.76087 35.492754 342 0 0 29.7625 36.75 343 0 0 28.356164 35.922374 344 0 0 28.455882 35.882353 345 0 0 26.22807 33.865497 346 0 0 27.803922 35.202614 347 0 0 28.565217 36.210145 348 0 0 26.648649 34.495495 349 0 0 24.545455 32.393939 350 0 0 26.366667 34.455556 351 0 0 30.703704 37.419753 352 0 0 30.304348 37.086957 353 0 0 29.6 37.2 354 0 0 27.352941 34.294118 355 0 0 29.733333 37.577778 356 0 0 27 34.944444 357 0 0 31.333333 38.407407 358 0 0 23.375 30.958333 359 0 0 31.625 37.416667 360 0 0 29.666667 36.388889 361 0 0 23.833333 33.611111 362 0 0 32.6 39.133333 363 0 0 29 36.111111 364 0 0 28.5 35.666667 365 0 0 24.5 34 366 0 0 29 37.333333 367 0 0 13.5 24.666667 368 0 0 16.5 30.5 369 0 0 26 36 370 0 0 11 31 371 0 0 14 30.333333 372 0 0 13 29.333333 373 0 0 13 31.666667 374 0 0 36 41 375 0 0 9 21.666667 376 0 0 14 25 377 0 0 36 41 378 0 0 36 41 379 0 0 11 20 380 0 0 32 38.666667 381 0 0 36 41 382 0 0 36 41 383 0 0 20 31.666667 384 0 0 29 37 385 0 0 9 21.666667