## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5381-Z0065-CTTGTGTCATGAGAT/441525-L5381-Z0065-CTTGTGTCATGAGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5381-Z0065-CTTGTGTCATGAGAT/441525-L5381-Z0065-CTTGTGTCATGAGAT_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 02:54:31 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 999078 999078 137 137065476 137065476 132425485 132425485 123353022 123353022 0 0 0.966148 0.899957 0 0.966148 0.899957 0 411196428 411196428 405061191 405061191 390680299 390680299 366026443 366026443 0.98508 0.950106 0.89015 0.98508 0.950106 0.89015 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 756 0 35.993841 40.995197 1 9849 0 35.987746 40.991374 2 12096 3923 35.995156 40.995914 3 30423 1110 35.98276 40.986021 4 50944 41898 35.990923 40.992552 5 99455 15056 35.995988 40.996671 6 106273 109554 35.980656 40.984744 7 179741 140949 35.980669 40.986742 8 185891 140215 35.988868 40.990467 9 224951 95594 35.960847 40.967123 10 233885 485372 35.882652 40.930602 11 276691 54672 35.915029 40.936855 12 330215 672591 35.266672 40.386898 13 337340 192940 33.897843 39.69537 14 429722 947297 35.888429 40.931976 15 353269 348835 35.832659 40.882826 16 370992 424570 35.784728 40.809447 17 504722 1083014 35.88042 40.897096 18 533095 681497 35.725252 40.77604 19 369681 696150 35.719083 40.790851 20 491539 996698 35.892239 40.927499 21 637730 1315216 35.811605 40.85906 22 318025 557245 35.586698 40.717156 23 1010142 1177843 35.24074 40.4496 24 564946 1145894 35.339858 40.54427 25 536706 479913 35.380211 40.578254 26 1745931 2440828 35.286492 40.494733 27 354232 873585 35.326251 40.54295 28 952557 368357 35.321595 40.540922 29 2460655 5025313 35.312743 40.530202 30 768396 39504 35.35957 40.564064 31 2341314 809081 35.360898 40.562555 32 1573726 5395654 35.327735 40.531462 33 843151 118967 35.359325 40.560516 34 2474816 2569059 35.36794 40.570316 35 2282766 3879798 35.376952 40.576531 36 113068853 2013804 35.398157 40.591738 37 0 4349224 35.400338 40.593526 38 0 373263 35.38564 40.585574 39 0 5105502 35.387165 40.584291 40 0 1 35.370399 40.571421 41 0 366026442 35.372846 40.571978 42 0 0 35.37195 40.571195 43 0 0 35.372526 40.573235 44 0 0 35.375922 40.574626 45 0 0 35.379749 40.577677 46 0 0 35.369235 40.568484 47 0 0 35.360813 40.561965 48 0 0 35.339131 40.546685 49 0 0 35.339504 40.547805 50 0 0 35.349242 40.555675 51 0 0 35.345991 40.553764 52 0 0 35.295635 40.518872 53 0 0 35.258684 40.506441 54 0 0 35.27455 40.511894 55 0 0 35.270519 40.509639 56 0 0 35.209406 40.482268 57 0 0 35.270789 40.505788 58 0 0 35.268224 40.498857 59 0 0 35.244643 40.481525 60 0 0 35.225925 40.466942 61 0 0 35.191522 40.441094 62 0 0 35.149899 40.409275 63 0 0 35.114473 40.382392 64 0 0 35.072143 40.35102 65 0 0 35.026139 40.316474 66 0 0 34.972921 40.278101 67 0 0 34.92017 40.238283 68 0 0 34.85594 40.191139 69 0 0 34.779436 40.134767 70 0 0 34.703397 40.074754 71 0 0 34.62405 40.009939 72 0 0 34.540942 39.943832 73 0 0 34.444017 39.868555 74 0 0 34.360211 39.800611 75 0 0 34.27066 39.733017 76 0 0 34.176921 39.659552 77 0 0 34.081062 39.587054 78 0 0 33.989618 39.518222 79 0 0 33.897039 39.446364 80 0 0 33.808429 39.374548 81 0 0 33.736611 39.314463 82 0 0 33.647376 39.242069 83 0 0 33.567055 39.179541 84 0 0 33.514104 39.137031 85 0 0 33.443019 39.080738 86 0 0 33.392099 39.03712 87 0 0 33.327069 38.986941 88 0 0 33.271966 38.941869 89 0 0 33.223243 38.899736 90 0 0 33.174366 38.85627 91 0 0 33.119978 38.81002 92 0 0 33.075006 38.768466 93 0 0 33.050947 38.748008 94 0 0 33.018843 38.720608 95 0 0 32.98656 38.69092 96 0 0 32.973269 38.679957 97 0 0 32.955247 38.666758 98 0 0 32.953082 38.662293 99 0 0 32.972047 38.678997 100 0 0 32.985822 38.68506 101 0 0 33.023378 38.713211 102 0 0 33.052178 38.737195 103 0 0 33.080106 38.755243 104 0 0 33.099355 38.767141 105 0 0 33.125227 38.783913 106 0 0 33.119789 38.778207 107 0 0 33.127029 38.783271 108 0 0 33.126503 38.783167 109 0 0 33.116792 38.775605 110 0 0 33.096606 38.759959 111 0 0 33.062247 38.733673 112 0 0 33.025058 38.700713 113 0 0 32.971713 38.653929 114 0 0 32.927076 38.616839 115 0 0 32.876421 38.576924 116 0 0 32.83937 38.549031 117 0 0 32.815132 38.533892 118 0 0 32.806797 38.531097 119 0 0 32.806147 38.533235 120 0 0 32.808972 38.537147 121 0 0 32.822994 38.543421 122 0 0 32.830784 38.546643 123 0 0 32.816184 38.531997 124 0 0 32.828917 38.543254 125 0 0 32.840877 38.548103 126 0 0 32.861075 38.560071 127 0 0 32.85886 38.559251 128 0 0 32.845698 38.54698 129 0 0 32.840754 38.539603 130 0 0 32.79807 38.503528 131 0 0 32.780294 38.489357 132 0 0 32.765106 38.473934 133 0 0 32.760087 38.468196 134 0 0 32.766811 38.470686 135 0 0 32.753866 38.458863 136 0 0 32.758638 38.464691 137 0 0 32.735418 38.444493 138 0 0 32.729116 38.443695 139 0 0 32.744102 38.456075 140 0 0 32.768334 38.476782 141 0 0 32.800703 38.503174 142 0 0 32.822243 38.519096 143 0 0 32.823557 38.514465 144 0 0 32.815422 38.507988 145 0 0 32.805037 38.494419 146 0 0 32.782992 38.477078 147 0 0 32.751411 38.450188 148 0 0 32.712199 38.416358 149 0 0 32.700738 38.404933 150 0 0 32.654875 38.369005 151 0 0 32.621365 38.34216 152 0 0 32.615061 38.334975 153 0 0 32.583815 38.313041 154 0 0 32.569217 38.29977 155 0 0 32.572353 38.301729 156 0 0 32.617025 38.340269 157 0 0 32.615178 38.339785 158 0 0 32.631831 38.34683 159 0 0 32.68012 38.388334 160 0 0 32.66943 38.376632 161 0 0 32.703444 38.401921 162 0 0 32.760058 38.4512 163 0 0 32.779482 38.462935 164 0 0 32.771245 38.458041 165 0 0 32.768937 38.456871 166 0 0 32.755436 38.443328 167 0 0 32.731476 38.417418 168 0 0 32.679149 38.369361 169 0 0 32.640889 38.337432 170 0 0 32.617055 38.318938 171 0 0 32.56948 38.281467 172 0 0 32.573061 38.287661 173 0 0 32.565214 38.280105 174 0 0 32.591577 38.299321 175 0 0 32.609555 38.319412 176 0 0 32.621305 38.329844 177 0 0 32.64995 38.356653 178 0 0 32.688937 38.385439 179 0 0 32.740009 38.430738 180 0 0 32.793332 38.473143 181 0 0 32.846363 38.516109 182 0 0 32.881977 38.549783 183 0 0 32.92395 38.587979 184 0 0 32.954393 38.606555 185 0 0 32.972258 38.62836 186 0 0 33.027439 38.665361 187 0 0 33.053698 38.68793 188 0 0 33.064393 38.697381 189 0 0 33.091618 38.715398 190 0 0 33.056085 38.690845 191 0 0 33.053876 38.695176 192 0 0 33.003742 38.665364 193 0 0 32.974047 38.646168 194 0 0 32.97389 38.655568 195 0 0 32.975325 38.658367 196 0 0 32.929379 38.629391 197 0 0 32.946682 38.651622 198 0 0 32.923802 38.642921 199 0 0 32.945917 38.663252 200 0 0 32.925863 38.666182 201 0 0 32.912689 38.654974 202 0 0 32.866068 38.628673 203 0 0 32.88904 38.648394 204 0 0 32.842829 38.62515 205 0 0 32.815181 38.611558 206 0 0 32.786992 38.59595 207 0 0 32.759524 38.579824 208 0 0 32.732961 38.563136 209 0 0 32.713798 38.546124 210 0 0 32.708971 38.550097 211 0 0 32.704034 38.545132 212 0 0 32.671421 38.524214 213 0 0 32.654777 38.526736 214 0 0 32.652613 38.521445 215 0 0 32.596179 38.492569 216 0 0 32.580663 38.481959 217 0 0 32.542232 38.454857 218 0 0 32.548042 38.460871 219 0 0 32.572007 38.483994 220 0 0 32.464789 38.407683 221 0 0 32.470424 38.413739 222 0 0 32.466995 38.413931 223 0 0 32.392325 38.367561 224 0 0 32.34264 38.336263 225 0 0 32.374003 38.351665 226 0 0 32.351534 38.345563 227 0 0 32.305341 38.314496 228 0 0 32.280669 38.293232 229 0 0 32.257616 38.272107 230 0 0 32.340169 38.346389 231 0 0 32.297746 38.312018 232 0 0 32.224321 38.238762 233 0 0 32.230306 38.259114 234 0 0 32.186045 38.235336 235 0 0 32.166811 38.215738 236 0 0 32.116487 38.191499 237 0 0 32.049232 38.145101 238 0 0 32.176716 38.240487 239 0 0 32.073181 38.170695 240 0 0 32.113437 38.220401 241 0 0 32.037573 38.147069 242 0 0 31.908817 38.061246 243 0 0 31.916363 38.058734 244 0 0 31.882152 38.036806 245 0 0 31.778757 37.958591 246 0 0 31.838645 38.010998 247 0 0 31.823835 38.009163 248 0 0 31.830466 38.01019 249 0 0 31.697681 37.933515 250 0 0 31.783952 37.994518 251 0 0 31.76752 37.966962 252 0 0 31.774847 37.980777 253 0 0 31.730512 37.972991 254 0 0 31.553102 37.853242 255 0 0 31.678277 37.934655 256 0 0 31.541925 37.83246 257 0 0 31.517101 37.841709 258 0 0 31.443422 37.804714 259 0 0 31.562674 37.886609 260 0 0 31.458859 37.785701 261 0 0 31.384397 37.711915 262 0 0 31.424007 37.749328 263 0 0 31.351838 37.710281 264 0 0 31.218531 37.673114 265 0 0 31.273924 37.69696 266 0 0 31.062892 37.522615 267 0 0 31.250466 37.681127 268 0 0 31.237182 37.626671 269 0 0 30.988349 37.47159 270 0 0 31.052428 37.525998 271 0 0 30.715178 37.346329 272 0 0 30.671833 37.281997 273 0 0 30.884072 37.40167 274 0 0 30.652343 37.289612 275 0 0 30.553308 37.231212 276 0 0 30.54907 37.197363 277 0 0 30.481055 37.155403 278 0 0 30.280209 36.939394 279 0 0 30.41686 37.142514 280 0 0 30.181147 36.984289 281 0 0 29.977011 36.823755 282 0 0 29.935045 36.839879 283 0 0 29.913887 36.873718 284 0 0 29.996808 36.822204 285 0 0 29.765749 36.734388 286 0 0 29.575458 36.52299 287 0 0 29.707395 36.683231 288 0 0 29.432073 36.431367 289 0 0 29.295313 36.310313 290 0 0 29.195659 36.298132 291 0 0 29.091552 36.171098 292 0 0 29.061103 36.181448 293 0 0 29.048246 36.194444 294 0 0 29.13341 36.281983 295 0 0 29.200478 36.28152 296 0 0 28.871613 36.051966 297 0 0 29.019974 36.111015 298 0 0 28.705988 35.958577 299 0 0 29.105064 36.150181 300 0 0 28.726547 35.93829 301 0 0 28.460603 35.673718 302 0 0 28.644284 35.942656 303 0 0 28.356349 35.735518 304 0 0 28.507426 35.740099 305 0 0 28.917051 36.053105 306 0 0 28.685315 35.906993 307 0 0 28.457207 35.848098 308 0 0 28.758814 35.967949 309 0 0 28.540357 35.745681 310 0 0 28.762477 35.969501 311 0 0 28.223541 35.623475 312 0 0 27.946764 35.375783 313 0 0 28.747748 35.886261 314 0 0 28.123021 35.519691 315 0 0 28.17976 35.62095 316 0 0 27.700288 35.216138 317 0 0 28.645312 35.905729 318 0 0 28.030405 35.508446 319 0 0 27.959184 35.505257 320 0 0 27.845528 35.21748 321 0 0 28.081678 35.514349 322 0 0 28.15 35.547619 323 0 0 28.354005 35.758829 324 0 0 27.495798 35.160598 325 0 0 28.17134 35.439252 326 0 0 28.69637 35.805281 327 0 0 28.187023 35.717557 328 0 0 28.222222 35.564103 329 0 0 27.6 35.023256 330 0 0 27.590674 35.376511 331 0 0 27.645714 35.386667 332 0 0 27.192308 34.737179 333 0 0 27.971429 35.235714 334 0 0 27.581197 34.62963 335 0 0 28.53271 35.844237 336 0 0 26.967033 34.505495 337 0 0 26.402439 34.154472 338 0 0 28.263889 35.407407 339 0 0 25.965517 34.132184 340 0 0 28.764706 36.169935 341 0 0 26.729167 34.784722 342 0 0 24.697674 33.310078 343 0 0 22.894737 31.149123 344 0 0 25.25 32.833333 345 0 0 29.115385 36.820513 346 0 0 28.285714 36.063492 347 0 0 21.8125 31 348 0 0 30.133333 36.377778 349 0 0 32 37.69697 350 0 0 29 36 351 0 0 28 35.083333 352 0 0 35.714286 40.714286 353 0 0 32.166667 38.388889 354 0 0 28.833333 34.277778 355 0 0 24.2 31 356 0 0 24 31.2 357 0 0 21.5 30.083333 358 0 0 28.5 35.083333 359 0 0 29.5 36.583333 360 0 0 21 29.666667 361 0 0 11 26.333333