## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5406-Z0096-CAGCCGATATCAGAT/441525-L5406-Z0096-CAGCCGATATCAGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5406-Z0096-CAGCCGATATCAGAT/441525-L5406-Z0096-CAGCCGATATCAGAT_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 03:02:01 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 132 132575677 132575677 127813302 127813302 118812393 118812393 0 0 0.964078 0.896185 0 0.964078 0.896185 0 397727031 397727031 391444336 391444336 377017854 377017854 352709468 352709468 0.984204 0.947931 0.886813 0.984204 0.947931 0.886813 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 782 0 35.991833 40.993909 1 9693 0 35.98741 40.991248 2 12001 3957 35.994206 40.995187 3 30064 1086 35.983632 40.986623 4 50308 42236 35.990521 40.992341 5 100743 16413 35.994356 40.995322 6 103257 110603 35.97605 40.979267 7 180579 143966 35.96906 40.97955 8 184960 136620 35.981369 40.984186 9 227425 98752 35.952775 40.959933 10 239903 473108 35.909825 40.943783 11 287093 55723 35.934789 40.952203 12 345826 676887 35.292219 40.402727 13 351072 199241 33.894616 39.696594 14 448254 975488 35.899406 40.93884 15 360453 362261 35.833333 40.883263 16 390400 444886 35.815848 40.836129 17 515464 1117520 35.903963 40.918677 18 550981 708054 35.793683 40.830575 19 373117 715894 35.783082 40.83943 20 490870 1013769 35.916051 40.944681 21 645202 1342106 35.869686 40.905947 22 318264 571133 35.67089 40.772984 23 992188 1151964 35.389622 40.579675 24 570483 1176611 35.376239 40.574587 25 528274 473063 35.387303 40.58486 26 1719116 2439252 35.326351 40.539125 27 356331 870059 35.334005 40.547762 28 943223 369002 35.352241 40.560456 29 2436958 5019523 35.344631 40.554477 30 749540 37739 35.342929 40.553003 31 2309254 789340 35.338891 40.548958 32 1546871 5426672 35.328161 40.539154 33 826733 114377 35.331739 40.543485 34 2402125 2505816 35.326253 40.540791 35 2190538 3856956 35.340689 40.549185 36 108787332 2001225 35.363769 40.565038 37 0 4269609 35.361784 40.566013 38 0 358870 35.357114 40.563574 39 0 4947782 35.354302 40.56121 40 0 0 35.352565 40.558979 41 0 352709468 35.333995 40.546153 42 0 0 35.33055 40.542696 43 0 0 35.33682 40.547459 44 0 0 35.346622 40.553784 45 0 0 35.349075 40.555695 46 0 0 35.346869 40.552866 47 0 0 35.332906 40.544769 48 0 0 35.328933 40.539797 49 0 0 35.329049 40.540855 50 0 0 35.323373 40.536158 51 0 0 35.310594 40.528253 52 0 0 35.299097 40.519548 53 0 0 35.283982 40.511198 54 0 0 35.280368 40.506662 55 0 0 35.26194 40.492764 56 0 0 35.245424 40.482209 57 0 0 35.237733 40.477832 58 0 0 35.226029 40.467461 59 0 0 35.190657 40.439956 60 0 0 35.158987 40.419698 61 0 0 35.127463 40.395157 62 0 0 35.088565 40.366375 63 0 0 35.051422 40.335563 64 0 0 34.991308 40.291848 65 0 0 34.936845 40.25214 66 0 0 34.873946 40.204773 67 0 0 34.804636 40.154501 68 0 0 34.725517 40.094191 69 0 0 34.634132 40.02509 70 0 0 34.529004 39.941929 71 0 0 34.430781 39.866106 72 0 0 34.323161 39.778092 73 0 0 34.194694 39.677223 74 0 0 34.078385 39.584147 75 0 0 33.960205 39.490872 76 0 0 33.845857 39.406717 77 0 0 33.731133 39.316374 78 0 0 33.61395 39.226819 79 0 0 33.512445 39.148427 80 0 0 33.414228 39.069229 81 0 0 33.316141 38.992345 82 0 0 33.247511 38.934448 83 0 0 33.178273 38.877868 84 0 0 33.109987 38.825342 85 0 0 33.059374 38.783157 86 0 0 33.010218 38.739444 87 0 0 32.956411 38.69835 88 0 0 32.902442 38.652432 89 0 0 32.862604 38.613887 90 0 0 32.802424 38.56287 91 0 0 32.767088 38.532613 92 0 0 32.72535 38.492886 93 0 0 32.695071 38.467889 94 0 0 32.673872 38.443505 95 0 0 32.640641 38.417763 96 0 0 32.628339 38.408227 97 0 0 32.619276 38.398218 98 0 0 32.607679 38.387716 99 0 0 32.622207 38.40016 100 0 0 32.645431 38.418229 101 0 0 32.681123 38.445337 102 0 0 32.725291 38.479747 103 0 0 32.759452 38.503238 104 0 0 32.794681 38.528645 105 0 0 32.816085 38.541018 106 0 0 32.837395 38.554277 107 0 0 32.82845 38.546288 108 0 0 32.835771 38.548212 109 0 0 32.829518 38.543218 110 0 0 32.800437 38.523946 111 0 0 32.767247 38.494872 112 0 0 32.746316 38.477588 113 0 0 32.679638 38.424361 114 0 0 32.630886 38.383523 115 0 0 32.594096 38.354401 116 0 0 32.572596 38.340649 117 0 0 32.540597 38.314873 118 0 0 32.548745 38.324143 119 0 0 32.551335 38.327389 120 0 0 32.561935 38.336449 121 0 0 32.587746 38.355114 122 0 0 32.60554 38.36748 123 0 0 32.619945 38.380735 124 0 0 32.656308 38.406594 125 0 0 32.678845 38.41876 126 0 0 32.708636 38.440062 127 0 0 32.703794 38.43327 128 0 0 32.700129 38.424386 129 0 0 32.679831 38.4063 130 0 0 32.676207 38.401663 131 0 0 32.63824 38.372294 132 0 0 32.627266 38.363495 133 0 0 32.638564 38.36933 134 0 0 32.616079 38.349934 135 0 0 32.612994 38.34776 136 0 0 32.59485 38.335579 137 0 0 32.604553 38.33862 138 0 0 32.626149 38.358941 139 0 0 32.629351 38.362183 140 0 0 32.66732 38.390889 141 0 0 32.709585 38.426413 142 0 0 32.717531 38.432817 143 0 0 32.692048 38.411575 144 0 0 32.699884 38.415639 145 0 0 32.715596 38.427327 146 0 0 32.681859 38.392149 147 0 0 32.652195 38.371686 148 0 0 32.629565 38.346367 149 0 0 32.595299 38.315307 150 0 0 32.551011 38.280244 151 0 0 32.524025 38.262154 152 0 0 32.512221 38.248045 153 0 0 32.49028 38.239126 154 0 0 32.507754 38.254203 155 0 0 32.498061 38.236623 156 0 0 32.534851 38.274299 157 0 0 32.538932 38.2751 158 0 0 32.546794 38.276972 159 0 0 32.594203 38.314419 160 0 0 32.637912 38.347709 161 0 0 32.660156 38.365592 162 0 0 32.696214 38.400698 163 0 0 32.741205 38.432367 164 0 0 32.75803 38.445607 165 0 0 32.763567 38.45159 166 0 0 32.7508 38.433458 167 0 0 32.728151 38.415256 168 0 0 32.726292 38.40646 169 0 0 32.664764 38.347778 170 0 0 32.6378 38.328832 171 0 0 32.613709 38.315294 172 0 0 32.575818 38.284033 173 0 0 32.613126 38.314387 174 0 0 32.618295 38.321636 175 0 0 32.622401 38.32637 176 0 0 32.673639 38.372559 177 0 0 32.70483 38.398333 178 0 0 32.761084 38.442499 179 0 0 32.793129 38.467473 180 0 0 32.843589 38.514353 181 0 0 32.886274 38.548123 182 0 0 32.929401 38.592426 183 0 0 33.003374 38.648064 184 0 0 33.025808 38.665787 185 0 0 33.01525 38.654361 186 0 0 33.091177 38.725799 187 0 0 33.112266 38.737319 188 0 0 33.097494 38.716582 189 0 0 33.119274 38.73983 190 0 0 33.125436 38.75036 191 0 0 33.125365 38.754311 192 0 0 33.097892 38.734506 193 0 0 33.047298 38.699636 194 0 0 33.027837 38.689033 195 0 0 33.021297 38.690083 196 0 0 33.059699 38.725773 197 0 0 33.018055 38.690705 198 0 0 33.04575 38.724699 199 0 0 33.036403 38.722417 200 0 0 33.027083 38.727213 201 0 0 33.039705 38.745208 202 0 0 32.965905 38.692478 203 0 0 32.973764 38.716545 204 0 0 32.944886 38.693766 205 0 0 32.966482 38.723203 206 0 0 32.941217 38.703837 207 0 0 32.944881 38.710617 208 0 0 32.913473 38.686708 209 0 0 32.840892 38.638458 210 0 0 32.847492 38.648467 211 0 0 32.905103 38.68657 212 0 0 32.881218 38.679019 213 0 0 32.841294 38.653576 214 0 0 32.792039 38.63106 215 0 0 32.81341 38.64055 216 0 0 32.777505 38.618089 217 0 0 32.764086 38.613918 218 0 0 32.782682 38.613634 219 0 0 32.708909 38.569538 220 0 0 32.643287 38.543523 221 0 0 32.656238 38.552633 222 0 0 32.589365 38.493739 223 0 0 32.626792 38.536392 224 0 0 32.63691 38.53698 225 0 0 32.6134 38.524492 226 0 0 32.577623 38.493536 227 0 0 32.524374 38.461999 228 0 0 32.513134 38.444915 229 0 0 32.408053 38.378055 230 0 0 32.542218 38.496728 231 0 0 32.563772 38.500039 232 0 0 32.545112 38.496976 233 0 0 32.467898 38.432912 234 0 0 32.376186 38.383934 235 0 0 32.372031 38.391899 236 0 0 32.390237 38.398572 237 0 0 32.328934 38.375557 238 0 0 32.325122 38.346027 239 0 0 32.30308 38.335045 240 0 0 32.288969 38.321208 241 0 0 32.263473 38.310418 242 0 0 32.275631 38.327563 243 0 0 32.263385 38.321923 244 0 0 32.234413 38.291061 245 0 0 32.113772 38.224089 246 0 0 32.09794 38.218785 247 0 0 32.11055 38.206842 248 0 0 32.167001 38.266678 249 0 0 31.983016 38.131418 250 0 0 32.10689 38.217287 251 0 0 31.932664 38.114831 252 0 0 31.996613 38.157236 253 0 0 32.060051 38.221285 254 0 0 31.910086 38.085344 255 0 0 31.99265 38.125494 256 0 0 32.012348 38.191836 257 0 0 31.816038 38.061982 258 0 0 31.842593 38.065897 259 0 0 31.872322 38.096677 260 0 0 31.814622 38.045433 261 0 0 31.868936 38.092288 262 0 0 31.692308 37.922363 263 0 0 31.618858 37.911932 264 0 0 31.716382 38.006632 265 0 0 31.634009 37.945538 266 0 0 31.494434 37.831676 267 0 0 31.309099 37.729767 268 0 0 31.32246 37.714011 269 0 0 31.415574 37.832267 270 0 0 31.357378 37.768116 271 0 0 31.209561 37.669921 272 0 0 31.038838 37.548605 273 0 0 31.049272 37.566895 274 0 0 31.016511 37.541338 275 0 0 30.778696 37.393388 276 0 0 30.698985 37.351058 277 0 0 30.594879 37.264794 278 0 0 30.624659 37.255365 279 0 0 30.505177 37.194013 280 0 0 30.402446 37.11213 281 0 0 30.276269 37.032884 282 0 0 30.224589 36.972726 283 0 0 30.154659 36.962396 284 0 0 29.816493 36.684428 285 0 0 30.048365 36.897139 286 0 0 30.017197 36.844914 287 0 0 29.942312 36.836313 288 0 0 29.765614 36.713201 289 0 0 29.762339 36.71484 290 0 0 29.582269 36.567666 291 0 0 29.527576 36.537261 292 0 0 29.682447 36.684293 293 0 0 29.440343 36.446447 294 0 0 29.315538 36.362064 295 0 0 29.288224 36.335183 296 0 0 29.19801 36.361896 297 0 0 29.088963 36.172798 298 0 0 29.284218 36.374534 299 0 0 29.076585 36.230854 300 0 0 29.305267 36.440472 301 0 0 28.819911 36.107514 302 0 0 29.10678 36.232486 303 0 0 28.658105 35.842929 304 0 0 29.02059 36.196849 305 0 0 29.058116 36.196894 306 0 0 28.917417 36.113111 307 0 0 28.893326 36.096406 308 0 0 28.631961 35.783495 309 0 0 28.882507 36.019582 310 0 0 28.47067 35.774674 311 0 0 28.816817 35.983233 312 0 0 28.117309 35.534865 313 0 0 28.942731 36.070778 314 0 0 28.88763 36.123387 315 0 0 28.220287 35.612705 316 0 0 28.500556 35.724509 317 0 0 28.445399 35.754192 318 0 0 28.203753 35.631367 319 0 0 28.728467 35.859367 320 0 0 28.868932 36.018878 321 0 0 27.456364 35.060606 322 0 0 28.628 35.924667 323 0 0 28.38512 35.654267 324 0 0 27.890215 35.422434 325 0 0 28.200528 35.228672 326 0 0 27.929619 35.242424 327 0 0 27.190323 34.772043 328 0 0 27.677193 35.330994 329 0 0 27.894531 35.279948 330 0 0 27.327434 34.89823 331 0 0 28.267677 35.895623 332 0 0 29.056497 36.122411 333 0 0 27.974684 35.504219 334 0 0 27.929078 35.475177 335 0 0 25.653543 33.60105 336 0 0 27.621622 35.132132 337 0 0 28.245098 35.359477 338 0 0 27.771739 35.065217 339 0 0 27.426667 35.053333 340 0 0 29.333333 36.280423 341 0 0 26.872727 34.115152 342 0 0 28.745098 35.803922 343 0 0 28.021739 35.586957 344 0 0 29.225 36.291667 345 0 0 25.257143 33.352381 346 0 0 26.5 35.055556 347 0 0 26.357143 34.345238 348 0 0 30.521739 37.15942 349 0 0 24.888889 34.518519 350 0 0 23.933333 32.844444 351 0 0 27.153846 34.589744 352 0 0 32 37.666667 353 0 0 26.857143 35 354 0 0 29.5 36.055556 355 0 0 28.333333 34.388889 356 0 0 24.8 33 357 0 0 32.2 38.066667 358 0 0 31.8 39.266667 359 0 0 28 33.222222 360 0 0 25 32.5 361 0 0 32.5 38 362 0 0 24 36.166667 363 0 0 36 41 364 0 0 30 36 365 0 0 26 32.166667 366 0 0 33.5 38.333333 367 0 0 31 38.5 368 0 0 34 39 369 0 0 24 33.666667 370 0 0 34 39 371 0 0 32 37 372 0 0 29 37 373 0 0 26 33