## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5266-Z0001-CAGCTCGAATGCGAT/441525-L5266-Z0001-CAGCTCGAATGCGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5266-Z0001-CAGCTCGAATGCGAT/441525-L5266-Z0001-CAGCTCGAATGCGAT_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 03:00:03 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 998951 998951 146 146623698 146623698 141636703 141636703 132050210 132050210 0 0 0.965988 0.900606 0 0.965988 0.900606 0 439871094 439871094 433332290 433332290 417996986 417996986 391908748 391908748 0.985135 0.950272 0.890963 0.985135 0.950272 0.890963 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 988 0 35.991385 40.99306 1 12440 0 35.953097 40.967534 2 14987 5344 35.98083 40.985609 3 37143 1392 35.969456 40.977921 4 57520 52513 35.98677 40.98986 5 117898 17713 35.990617 40.992968 6 108069 135585 35.964638 40.969984 7 206233 167319 35.970307 40.979544 8 191074 150996 35.983633 40.987335 9 246163 115038 35.951681 40.95961 10 256847 513824 35.881563 40.92804 11 301860 65293 35.920376 40.94115 12 354331 722818 35.33361 40.438383 13 353383 201151 33.989741 39.755495 14 467794 996551 35.881503 40.926917 15 385421 383020 35.828729 40.881059 16 385928 426300 35.81658 40.840429 17 532840 1111839 35.916172 40.930973 18 563243 753529 35.708519 40.761051 19 392833 718579 35.780587 40.836276 20 542907 1012553 35.921589 40.946742 21 689984 1440248 35.834482 40.879705 22 349491 568972 35.605277 40.732715 23 1106187 1316022 35.290627 40.517608 24 610482 1265880 35.321877 40.540355 25 559331 511346 35.317952 40.537936 26 1825590 2609295 35.260263 40.491736 27 383321 943927 35.286347 40.516511 28 982507 423810 35.293967 40.52346 29 2536693 5243251 35.283498 40.514305 30 823018 42694 35.285598 40.515197 31 2506866 924272 35.279594 40.508701 32 1757372 5562429 35.279326 40.506757 33 908976 133805 35.274864 40.505648 34 2623243 2930721 35.272995 40.506051 35 2377250 3971571 35.291939 40.517175 36 121053485 2314437 35.311334 40.531942 37 0 4442695 35.315022 40.535981 38 0 436091 35.303874 40.528645 39 0 5329523 35.305071 40.528762 40 0 1 35.293958 40.520954 41 0 391908747 35.281902 40.510733 42 0 0 35.276292 40.508109 43 0 0 35.280645 40.511596 44 0 0 35.293329 40.51955 45 0 0 35.297286 40.520914 46 0 0 35.288836 40.515968 47 0 0 35.279151 40.508381 48 0 0 35.269358 40.502428 49 0 0 35.266539 40.500088 50 0 0 35.268499 40.501414 51 0 0 35.263675 40.49728 52 0 0 35.246867 40.487137 53 0 0 35.235037 40.481133 54 0 0 35.234661 40.479558 55 0 0 35.219211 40.468003 56 0 0 35.206686 40.463166 57 0 0 35.210773 40.461792 58 0 0 35.185524 40.44282 59 0 0 35.164857 40.427313 60 0 0 35.142857 40.410062 61 0 0 35.09902 40.378412 62 0 0 35.058606 40.346795 63 0 0 35.018048 40.316816 64 0 0 34.975239 40.28477 65 0 0 34.913617 40.236844 66 0 0 34.864336 40.200635 67 0 0 34.796157 40.149925 68 0 0 34.725082 40.097081 69 0 0 34.655755 40.042346 70 0 0 34.576738 39.979664 71 0 0 34.499232 39.919436 72 0 0 34.413965 39.850905 73 0 0 34.330036 39.785226 74 0 0 34.247743 39.718582 75 0 0 34.174708 39.658886 76 0 0 34.10073 39.603753 77 0 0 34.03591 39.554352 78 0 0 33.971077 39.502634 79 0 0 33.918598 39.462273 80 0 0 33.85342 39.40942 81 0 0 33.810901 39.37223 82 0 0 33.766127 39.33695 83 0 0 33.732181 39.30857 84 0 0 33.698415 39.281962 85 0 0 33.665555 39.252311 86 0 0 33.630326 39.223462 87 0 0 33.592842 39.192306 88 0 0 33.563943 39.166343 89 0 0 33.526516 39.133943 90 0 0 33.477863 39.092977 91 0 0 33.44214 39.061822 92 0 0 33.408307 39.033655 93 0 0 33.373417 39.005293 94 0 0 33.347726 38.979951 95 0 0 33.328807 38.963874 96 0 0 33.309854 38.950036 97 0 0 33.290704 38.93345 98 0 0 33.29861 38.938281 99 0 0 33.305365 38.944003 100 0 0 33.325829 38.960008 101 0 0 33.358327 38.984691 102 0 0 33.375038 38.997066 103 0 0 33.405741 39.022404 104 0 0 33.422133 39.032582 105 0 0 33.438232 39.042169 106 0 0 33.429638 39.031271 107 0 0 33.425346 39.024955 108 0 0 33.412036 39.015927 109 0 0 33.390274 38.997933 110 0 0 33.367738 38.980226 111 0 0 33.318853 38.941585 112 0 0 33.272667 38.902201 113 0 0 33.228194 38.864278 114 0 0 33.1741 38.822048 115 0 0 33.11744 38.77682 116 0 0 33.101166 38.763289 117 0 0 33.080308 38.745361 118 0 0 33.075 38.742618 119 0 0 33.075111 38.74871 120 0 0 33.086807 38.757341 121 0 0 33.098022 38.763102 122 0 0 33.102498 38.770114 123 0 0 33.112425 38.772384 124 0 0 33.127695 38.783409 125 0 0 33.145901 38.794395 126 0 0 33.142602 38.78792 127 0 0 33.153959 38.79074 128 0 0 33.149958 38.784353 129 0 0 33.13261 38.769044 130 0 0 33.089709 38.736328 131 0 0 33.074568 38.723183 132 0 0 33.060937 38.709816 133 0 0 33.052929 38.707101 134 0 0 33.04219 38.68981 135 0 0 33.044561 38.693105 136 0 0 33.030313 38.680177 137 0 0 33.018455 38.674296 138 0 0 33.02682 38.67894 139 0 0 33.034778 38.689165 140 0 0 33.071413 38.721136 141 0 0 33.085218 38.728971 142 0 0 33.120862 38.756926 143 0 0 33.120784 38.755556 144 0 0 33.102975 38.740881 145 0 0 33.106104 38.741912 146 0 0 33.076196 38.716267 147 0 0 33.049032 38.687627 148 0 0 33.013264 38.658946 149 0 0 32.969847 38.622817 150 0 0 32.935772 38.594984 151 0 0 32.913642 38.578236 152 0 0 32.88386 38.55755 153 0 0 32.875227 38.550094 154 0 0 32.897833 38.566279 155 0 0 32.880631 38.553852 156 0 0 32.89852 38.566876 157 0 0 32.930651 38.591168 158 0 0 32.957627 38.613256 159 0 0 32.989809 38.634136 160 0 0 33.010649 38.654 161 0 0 33.057506 38.692948 162 0 0 33.077094 38.705762 163 0 0 33.098581 38.72133 164 0 0 33.118055 38.741771 165 0 0 33.103967 38.72588 166 0 0 33.125047 38.740546 167 0 0 33.092417 38.709944 168 0 0 33.071168 38.689392 169 0 0 33.009529 38.637712 170 0 0 32.986433 38.616365 171 0 0 32.963704 38.602195 172 0 0 32.962978 38.600826 173 0 0 32.962174 38.600614 174 0 0 32.979022 38.616496 175 0 0 32.959318 38.602526 176 0 0 33.006975 38.646984 177 0 0 33.020167 38.654573 178 0 0 33.082085 38.706576 179 0 0 33.114277 38.731381 180 0 0 33.162821 38.77924 181 0 0 33.191266 38.799365 182 0 0 33.240317 38.841409 183 0 0 33.255033 38.85578 184 0 0 33.289774 38.885972 185 0 0 33.304899 38.898387 186 0 0 33.332076 38.922201 187 0 0 33.332058 38.923188 188 0 0 33.327854 38.916546 189 0 0 33.363355 38.949071 190 0 0 33.381913 38.966972 191 0 0 33.33529 38.926086 192 0 0 33.324227 38.926129 193 0 0 33.314958 38.921596 194 0 0 33.250709 38.87607 195 0 0 33.259612 38.893234 196 0 0 33.248709 38.884397 197 0 0 33.254273 38.898296 198 0 0 33.225575 38.88399 199 0 0 33.200623 38.875993 200 0 0 33.239119 38.903116 201 0 0 33.240127 38.908483 202 0 0 33.21325 38.897496 203 0 0 33.223917 38.910359 204 0 0 33.197995 38.896302 205 0 0 33.195602 38.898681 206 0 0 33.172208 38.884598 207 0 0 33.144338 38.872522 208 0 0 33.143419 38.875819 209 0 0 33.141837 38.876623 210 0 0 33.103954 38.854886 211 0 0 33.061385 38.828937 212 0 0 33.083434 38.846099 213 0 0 33.089878 38.849748 214 0 0 33.046462 38.823024 215 0 0 33.018146 38.805118 216 0 0 33.017845 38.808206 217 0 0 33.012125 38.810266 218 0 0 32.955834 38.775107 219 0 0 32.928843 38.763245 220 0 0 32.943307 38.763616 221 0 0 32.899243 38.737813 222 0 0 32.892939 38.73883 223 0 0 32.871637 38.726928 224 0 0 32.860088 38.712953 225 0 0 32.815159 38.691618 226 0 0 32.823776 38.704394 227 0 0 32.801461 38.68255 228 0 0 32.768749 38.66006 229 0 0 32.759068 38.650491 230 0 0 32.680498 38.599271 231 0 0 32.689665 38.606174 232 0 0 32.675974 38.59648 233 0 0 32.667251 38.608595 234 0 0 32.608659 38.563213 235 0 0 32.615173 38.569924 236 0 0 32.620493 38.576659 237 0 0 32.555836 38.525728 238 0 0 32.554438 38.526699 239 0 0 32.536647 38.519758 240 0 0 32.487391 38.481211 241 0 0 32.505513 38.504771 242 0 0 32.450525 38.456943 243 0 0 32.417751 38.432484 244 0 0 32.369775 38.400849 245 0 0 32.336943 38.387301 246 0 0 32.247315 38.333659 247 0 0 32.285532 38.355454 248 0 0 32.19812 38.308343 249 0 0 32.23822 38.353161 250 0 0 32.174293 38.298551 251 0 0 32.12377 38.247798 252 0 0 32.127429 38.263125 253 0 0 32.109019 38.256203 254 0 0 32.05844 38.20162 255 0 0 32.053903 38.206522 256 0 0 31.98851 38.161364 257 0 0 31.869464 38.091463 258 0 0 31.871295 38.093534 259 0 0 31.841019 38.084679 260 0 0 31.688495 37.986086 261 0 0 31.733767 37.992687 262 0 0 31.684031 37.968088 263 0 0 31.670872 37.970562 264 0 0 31.528686 37.857681 265 0 0 31.581586 37.905997 266 0 0 31.444053 37.804761 267 0 0 31.429139 37.794094 268 0 0 31.352915 37.752385 269 0 0 31.309277 37.729328 270 0 0 31.26716 37.706698 271 0 0 31.130837 37.623502 272 0 0 31.020318 37.53453 273 0 0 31.056115 37.549225 274 0 0 30.995038 37.543839 275 0 0 30.919243 37.458289 276 0 0 30.854349 37.403813 277 0 0 30.721262 37.330838 278 0 0 30.701033 37.311923 279 0 0 30.648251 37.301565 280 0 0 30.55498 37.220347 281 0 0 30.38066 37.123326 282 0 0 30.368715 37.08746 283 0 0 30.293077 37.052638 284 0 0 30.288753 37.074491 285 0 0 30.171964 36.97752 286 0 0 30.03689 36.84766 287 0 0 30.091077 36.905362 288 0 0 30.005985 36.843418 289 0 0 29.936149 36.790541 290 0 0 29.884787 36.762767 291 0 0 29.884231 36.774987 292 0 0 29.90519 36.781392 293 0 0 29.884619 36.759959 294 0 0 29.799896 36.677682 295 0 0 29.655686 36.601293 296 0 0 29.468232 36.492485 297 0 0 29.404493 36.424067 298 0 0 29.466232 36.463627 299 0 0 29.334791 36.358977 300 0 0 29.431538 36.416649 301 0 0 29.247403 36.298291 302 0 0 29.231469 36.329156 303 0 0 29.249564 36.328391 304 0 0 28.801832 36.016361 305 0 0 28.868352 36.091475 306 0 0 28.827666 36.050113 307 0 0 28.874369 36.035603 308 0 0 28.741873 35.974426 309 0 0 28.430223 35.738198 310 0 0 28.555229 35.80263 311 0 0 28.522517 35.77745 312 0 0 28.720067 35.921787 313 0 0 28.456081 35.805781 314 0 0 28.454325 35.766739 315 0 0 28.284749 35.593834 316 0 0 28.643357 35.898182 317 0 0 28.489187 35.73642 318 0 0 28.37207 35.667767 319 0 0 28.226395 35.587744 320 0 0 28.277024 35.650523 321 0 0 28.561242 35.827601 322 0 0 27.793419 35.295247 323 0 0 28.071321 35.469781 324 0 0 28.251104 35.59014 325 0 0 28.493873 35.758987 326 0 0 28.420231 35.73976 327 0 0 28.482784 35.806637 328 0 0 28.342409 35.689494 329 0 0 27.924424 35.367127 330 0 0 28.296748 35.751694 331 0 0 27.946893 35.270056 332 0 0 28.03607 35.402985 333 0 0 28.453665 35.840018 334 0 0 28.14486 35.441848 335 0 0 28.069149 35.470449 336 0 0 27.641434 35.167995 337 0 0 27.661364 35.193182 338 0 0 27.596447 35.200508 339 0 0 27.79646 35.111111 340 0 0 26.847134 34.791932 341 0 0 27.899628 35.483271 342 0 0 29.185345 36.275862 343 0 0 27.339806 34.823625 344 0 0 27.544944 35.230337 345 0 0 28.060811 35.813063 346 0 0 27.055556 34.632275 347 0 0 27.571429 34.85119 348 0 0 26.653061 35.098639 349 0 0 27.065217 34.757246 350 0 0 26.269231 34.709402 351 0 0 29.102941 36.411765 352 0 0 28.903226 36.026882 353 0 0 25.611111 34.123457 354 0 0 27.714286 35.537415 355 0 0 28.604651 35.658915 356 0 0 28.944444 36.111111 357 0 0 29.352941 36.058824 358 0 0 27.935484 35.064516 359 0 0 28.344828 35.16092 360 0 0 28.740741 36.074074 361 0 0 24.772727 33.621212 362 0 0 26.647059 34.72549 363 0 0 31.5 37.071429 364 0 0 31.75 37.833333 365 0 0 29.333333 37.027778 366 0 0 30.888889 37.296296 367 0 0 26.222222 33.592593 368 0 0 29.555556 36.259259 369 0 0 27.25 34.833333 370 0 0 25.333333 32 371 0 0 31.6 37.4 372 0 0 33.25 38.75 373 0 0 29.25 35.833333 374 0 0 24 33.666667 375 0 0 30 36.25 376 0 0 34.25 39.5 377 0 0 18.333333 26.444444 378 0 0 36 40.777778 379 0 0 36 40.777778 380 0 0 35 40 381 0 0 36 41 382 0 0 31 38 383 0 0 36 41 384 0 0 3 20 385 0 0 23 35