## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5379-Z0063-CACACTTGATGCGAT/441525-L5379-Z0063-CACACTTGATGCGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5379-Z0063-CACACTTGATGCGAT/441525-L5379-Z0063-CACACTTGATGCGAT_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 02:56:36 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 999427 999427 127 127799358 127799358 123118904 123118904 114072084 114072084 0 0 0.963377 0.892587 0 0.963377 0.892587 0 383398074 383398074 377187202 377187202 362827671 362827671 338715677 338715677 0.9838 0.946347 0.883457 0.9838 0.946347 0.883457 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 761 0 35.995452 40.996696 1 9535 0 35.989763 40.993231 2 11899 3648 35.993838 40.994758 3 29739 1034 35.980067 40.983991 4 49194 40946 35.990088 40.991978 5 97309 15523 35.993538 40.994608 6 106149 107229 35.977894 40.981466 7 175589 139555 35.975802 40.983592 8 190339 136754 35.985095 40.987553 9 224900 96410 35.959788 40.965995 10 236835 480154 35.888795 40.933015 11 282646 53912 35.922226 40.942162 12 335863 676633 35.207689 40.332816 13 347386 196586 33.668344 39.555195 14 436736 961356 35.890277 40.932014 15 355819 351088 35.857994 40.901567 16 382275 446120 35.843161 40.863849 17 508156 1102953 35.915267 40.929071 18 532042 691844 35.745341 40.790665 19 367282 709127 35.75274 40.81558 20 482613 1016549 35.90535 40.937315 21 633356 1302916 35.849485 40.89196 22 310125 564053 35.627341 40.748788 23 991626 1163520 35.355287 40.563221 24 560428 1119922 35.355927 40.566434 25 539594 467054 35.366034 40.571327 26 1739386 2457364 35.304189 40.526177 27 346441 839321 35.324396 40.543841 28 965680 359507 35.34598 40.556828 29 2477571 5069325 35.3376 40.551367 30 741189 37874 35.332727 40.548049 31 2334867 749704 35.335504 40.547978 32 1518716 5475258 35.324998 40.540017 33 812045 110526 35.333755 40.546698 34 2395829 2469456 35.327433 40.542771 35 2156535 3850905 35.344303 40.553535 36 104112903 1922898 35.365409 40.568967 37 0 4261384 35.366838 40.571621 38 0 333724 35.357184 40.563711 39 0 4900265 35.361878 40.567538 40 0 0 35.35416 40.560997 41 0 338715677 35.344606 40.553907 42 0 0 35.331735 40.54598 43 0 0 35.337972 40.548862 44 0 0 35.348553 40.555073 45 0 0 35.348353 40.555545 46 0 0 35.343602 40.552183 47 0 0 35.336598 40.547579 48 0 0 35.32439 40.538362 49 0 0 35.320049 40.535221 50 0 0 35.312976 40.531563 51 0 0 35.305062 40.525058 52 0 0 35.28961 40.514389 53 0 0 35.270399 40.503848 54 0 0 35.260431 40.496251 55 0 0 35.246442 40.484673 56 0 0 35.212886 40.46278 57 0 0 35.194658 40.445296 58 0 0 35.162341 40.421235 59 0 0 35.110915 40.384267 60 0 0 35.055573 40.343545 61 0 0 34.995936 40.297878 62 0 0 34.922966 40.239931 63 0 0 34.844269 40.180355 64 0 0 34.757678 40.113663 65 0 0 34.652454 40.037243 66 0 0 34.561916 39.967401 67 0 0 34.432339 39.870346 68 0 0 34.316213 39.783401 69 0 0 34.183887 39.680145 70 0 0 34.046258 39.569826 71 0 0 33.919077 39.469616 72 0 0 33.778457 39.355483 73 0 0 33.647693 39.250988 74 0 0 33.515872 39.146292 75 0 0 33.416447 39.070533 76 0 0 33.309206 38.985557 77 0 0 33.216719 38.917512 78 0 0 33.142901 38.860891 79 0 0 33.078432 38.808502 80 0 0 33.025398 38.762387 81 0 0 32.986331 38.729542 82 0 0 32.951885 38.696622 83 0 0 32.924629 38.67527 84 0 0 32.911103 38.660468 85 0 0 32.883821 38.639094 86 0 0 32.871687 38.624147 87 0 0 32.844499 38.600266 88 0 0 32.809044 38.570402 89 0 0 32.780924 38.54526 90 0 0 32.732961 38.502748 91 0 0 32.692049 38.466269 92 0 0 32.660757 38.436407 93 0 0 32.617973 38.401004 94 0 0 32.577025 38.368035 95 0 0 32.546479 38.342314 96 0 0 32.51733 38.320612 97 0 0 32.500153 38.306939 98 0 0 32.484929 38.295237 99 0 0 32.510378 38.314619 100 0 0 32.53598 38.33128 101 0 0 32.586746 38.37296 102 0 0 32.628681 38.404347 103 0 0 32.672958 38.438308 104 0 0 32.707098 38.463628 105 0 0 32.731171 38.477364 106 0 0 32.766409 38.502036 107 0 0 32.762676 38.494125 108 0 0 32.773135 38.503275 109 0 0 32.760969 38.496686 110 0 0 32.760917 38.494526 111 0 0 32.728722 38.46814 112 0 0 32.702953 38.446252 113 0 0 32.661237 38.406579 114 0 0 32.613239 38.372468 115 0 0 32.571718 38.335749 116 0 0 32.523746 38.302318 117 0 0 32.515468 38.295897 118 0 0 32.518554 38.301711 119 0 0 32.509437 38.296874 120 0 0 32.543735 38.325065 121 0 0 32.544581 38.320077 122 0 0 32.542231 38.318366 123 0 0 32.540154 38.318447 124 0 0 32.557873 38.327228 125 0 0 32.580599 38.343286 126 0 0 32.593462 38.350307 127 0 0 32.596573 38.348575 128 0 0 32.571429 38.325008 129 0 0 32.537549 38.297546 130 0 0 32.535548 38.292574 131 0 0 32.510407 38.271731 132 0 0 32.482763 38.250502 133 0 0 32.484159 38.249728 134 0 0 32.497082 38.259162 135 0 0 32.488826 38.247249 136 0 0 32.492291 38.251742 137 0 0 32.489641 38.247818 138 0 0 32.467578 38.235115 139 0 0 32.495272 38.255875 140 0 0 32.525733 38.28128 141 0 0 32.550118 38.295916 142 0 0 32.549241 38.293493 143 0 0 32.555877 38.297071 144 0 0 32.582446 38.320535 145 0 0 32.5561 38.292658 146 0 0 32.528844 38.269912 147 0 0 32.513478 38.255087 148 0 0 32.483394 38.230846 149 0 0 32.449033 38.199368 150 0 0 32.436584 38.187179 151 0 0 32.413499 38.167469 152 0 0 32.377246 38.143367 153 0 0 32.356611 38.133083 154 0 0 32.357583 38.134148 155 0 0 32.386047 38.149935 156 0 0 32.393782 38.160323 157 0 0 32.416768 38.1766 158 0 0 32.438231 38.194329 159 0 0 32.505798 38.246082 160 0 0 32.517909 38.255129 161 0 0 32.530343 38.265952 162 0 0 32.568884 38.300911 163 0 0 32.601038 38.322065 164 0 0 32.599557 38.325987 165 0 0 32.609913 38.33311 166 0 0 32.610782 38.32785 167 0 0 32.612791 38.326498 168 0 0 32.579198 38.28779 169 0 0 32.555669 38.268059 170 0 0 32.50459 38.227744 171 0 0 32.50504 38.230886 172 0 0 32.496889 38.226084 173 0 0 32.537443 38.263884 174 0 0 32.530075 38.25236 175 0 0 32.57778 38.296079 176 0 0 32.600615 38.32508 177 0 0 32.616903 38.336087 178 0 0 32.659902 38.369849 179 0 0 32.731228 38.426107 180 0 0 32.744714 38.444716 181 0 0 32.813564 38.496244 182 0 0 32.867527 38.536357 183 0 0 32.931923 38.59143 184 0 0 32.951359 38.614074 185 0 0 32.982827 38.646159 186 0 0 32.995388 38.650708 187 0 0 33.028401 38.677515 188 0 0 33.022326 38.678966 189 0 0 33.039566 38.693716 190 0 0 33.013582 38.667903 191 0 0 32.995932 38.657803 192 0 0 32.973465 38.6484 193 0 0 32.978288 38.657298 194 0 0 32.944184 38.637544 195 0 0 32.925292 38.627234 196 0 0 32.907529 38.621001 197 0 0 32.912757 38.628851 198 0 0 32.897008 38.619661 199 0 0 32.901778 38.640786 200 0 0 32.932628 38.665023 201 0 0 32.886715 38.638939 202 0 0 32.881691 38.634159 203 0 0 32.835772 38.617917 204 0 0 32.839605 38.616658 205 0 0 32.797598 38.608207 206 0 0 32.76796 38.583248 207 0 0 32.783098 38.596925 208 0 0 32.758072 38.576454 209 0 0 32.715476 38.553881 210 0 0 32.760843 38.580294 211 0 0 32.71742 38.546904 212 0 0 32.717633 38.567873 213 0 0 32.727227 38.567823 214 0 0 32.70114 38.554491 215 0 0 32.690985 38.542851 216 0 0 32.632898 38.516562 217 0 0 32.634082 38.50289 218 0 0 32.523933 38.451925 219 0 0 32.584256 38.493218 220 0 0 32.491876 38.428211 221 0 0 32.50084 38.441878 222 0 0 32.444101 38.388029 223 0 0 32.458267 38.404711 224 0 0 32.376304 38.355388 225 0 0 32.413074 38.36829 226 0 0 32.374079 38.360361 227 0 0 32.377322 38.361722 228 0 0 32.412066 38.401139 229 0 0 32.365709 38.35017 230 0 0 32.322995 38.319527 231 0 0 32.249838 38.278168 232 0 0 32.337448 38.339089 233 0 0 32.102194 38.164557 234 0 0 32.20851 38.244358 235 0 0 32.22711 38.279042 236 0 0 32.185253 38.214953 237 0 0 32.225543 38.278736 238 0 0 32.162937 38.235267 239 0 0 32.015536 38.14375 240 0 0 32.073682 38.167069 241 0 0 31.968669 38.093 242 0 0 31.934622 38.092054 243 0 0 32.010909 38.132571 244 0 0 31.814269 37.984576 245 0 0 31.782779 37.962214 246 0 0 31.891757 38.05661 247 0 0 31.652122 37.910125 248 0 0 31.720363 37.934818 249 0 0 31.740545 37.954219 250 0 0 31.635305 37.859074 251 0 0 31.515421 37.836066 252 0 0 31.560046 37.848027 253 0 0 31.561542 37.831919 254 0 0 31.537797 37.85092 255 0 0 31.485264 37.792151 256 0 0 31.437407 37.769315 257 0 0 31.393945 37.744401 258 0 0 31.227384 37.599696 259 0 0 31.42746 37.753075 260 0 0 31.440381 37.78068 261 0 0 31.327497 37.685844 262 0 0 31.265488 37.625629 263 0 0 31.289302 37.664081 264 0 0 31.018266 37.473861 265 0 0 31.202199 37.618165 266 0 0 31.117399 37.585664 267 0 0 31.004349 37.49958 268 0 0 31.147274 37.586736 269 0 0 30.769903 37.340372 270 0 0 30.966891 37.45714 271 0 0 30.909671 37.463979 272 0 0 30.901309 37.428185 273 0 0 30.40881 37.083535 274 0 0 30.619126 37.259778 275 0 0 30.602825 37.245198 276 0 0 30.519616 37.234719 277 0 0 30.25739 36.981089 278 0 0 30.385442 37.119472 279 0 0 30.218239 36.97935 280 0 0 29.992866 36.815607 281 0 0 30.198195 36.964795 282 0 0 29.839931 36.745726 283 0 0 29.732149 36.673416 284 0 0 29.691149 36.646101 285 0 0 30.130435 36.953187 286 0 0 29.640625 36.667869 287 0 0 29.540597 36.505109 288 0 0 29.682842 36.606586 289 0 0 29.542999 36.553354 290 0 0 29.388889 36.473389 291 0 0 29.451754 36.491391 292 0 0 29.484787 36.528059 293 0 0 29.318787 36.322867 294 0 0 29.206992 36.349982 295 0 0 29.086705 36.124277 296 0 0 29.239539 36.344855 297 0 0 29.187023 36.260602 298 0 0 29.120296 36.192428 299 0 0 28.93338 36.079009 300 0 0 29.080383 36.240413 301 0 0 28.821759 36.014146 302 0 0 28.776241 36.021155 303 0 0 28.577222 35.831464 304 0 0 28.566331 35.820372 305 0 0 29.354269 36.324501 306 0 0 29.059856 36.227726 307 0 0 28.479826 35.840058 308 0 0 28.767773 35.924171 309 0 0 28.684879 35.879288 310 0 0 28.681452 35.885753 311 0 0 28.504335 35.861753 312 0 0 28.388535 35.666136 313 0 0 28.114923 35.643796 314 0 0 28.22366 35.783734 315 0 0 27.781818 35.315152 316 0 0 28.787554 35.849785 317 0 0 28.361305 35.939394 318 0 0 29.01519 36.145148 319 0 0 27.610959 34.961644 320 0 0 28.46319 35.699387 321 0 0 28.190311 35.626298 322 0 0 27.778195 35.313283 323 0 0 27.825911 35.090418 324 0 0 28.091703 35.416303 325 0 0 27.761905 34.922222 326 0 0 27.927083 35.402778 327 0 0 26.74269 34.489279 328 0 0 27.275168 34.825503 329 0 0 27.767442 35.281654 330 0 0 26.725664 34.705015 331 0 0 26.455446 33.937294 332 0 0 28.022222 35.485185 333 0 0 29.775 36.733333 334 0 0 28.486111 35.837963 335 0 0 26.590909 34.454545 336 0 0 29.160714 36.720238 337 0 0 29.377778 36.177778 338 0 0 28.461538 35.504274 339 0 0 25.647059 34.303922 340 0 0 26.566667 33.855556 341 0 0 28.285714 35.571429 342 0 0 27.888889 35.604938 343 0 0 28.684211 36.140351 344 0 0 26.9375 34.25 345 0 0 27.933333 35.911111 346 0 0 23.5 32.583333 347 0 0 31.7 38.6 348 0 0 21.6 32.9 349 0 0 27.222222 35.481481 350 0 0 28.666667 35.444444 351 0 0 32.714286 38.428571 352 0 0 25.428571 33.190476 353 0 0 27.333333 34.166667 354 0 0 30 35.333333 355 0 0 32.6 38.333333 356 0 0 29 36.8 357 0 0 22.25 29.916667 358 0 0 19.5 28.5 359 0 0 30.5 37.75 360 0 0 32.333333 38.888889 361 0 0 10.5 21 362 0 0 20 30.833333 363 0 0 23 31.666667 364 0 0 35 39.666667 365 0 0 36 41 366 0 0 14 23.333333 367 0 0 9 21.666667 368 0 0 26 36 369 0 0 20 25 370 0 0 31 38 371 0 0 29 35 372 0 0 31 38