## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5396-Z0083-CAGTGTATTGCTGAT/441525-L5396-Z0083-CAGTGTATTGCTGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5396-Z0083-CAGTGTATTGCTGAT/441525-L5396-Z0083-CAGTGTATTGCTGAT_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 02:59:56 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 998354 998354 125 125334372 125334372 120387732 120387732 111216272 111216272 0 0 0.960532 0.887357 0 0.960532 0.887357 0 376003116 376003116 369446618 369446618 354736232 354736232 330374324 330374324 0.982563 0.94344 0.878648 0.982563 0.94344 0.878648 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 890 0 35.991812 40.993695 1 11085 0 35.984527 40.98928 2 13404 4364 35.994343 40.995184 3 34446 1226 35.980724 40.9841 4 55187 47597 35.990946 40.992632 5 110950 18302 35.9958 40.996549 6 110519 123788 35.977216 40.980764 7 195109 158613 35.977617 40.984809 8 194480 148181 35.986297 40.988852 9 240011 111424 35.959001 40.965491 10 255127 504173 35.89869 40.935993 11 301973 61831 35.940193 40.955664 12 359302 712944 35.18534 40.312772 13 359062 212689 33.582876 39.50019 14 469585 1010760 35.897778 40.937969 15 377136 379130 35.822004 40.874425 16 399315 460714 35.789247 40.811536 17 523816 1136536 35.897036 40.910853 18 562669 743622 35.744964 40.790173 19 372574 720604 35.754101 40.819528 20 508524 1020705 35.907715 40.939107 21 666549 1379460 35.826741 40.874031 22 322028 567268 35.570198 40.70526 23 1034212 1198776 35.237791 40.469363 24 574580 1189783 35.248846 40.487447 25 537505 475824 35.26113 40.497507 26 1756157 2531477 35.181827 40.43646 27 362245 868986 35.201927 40.45784 28 950371 377920 35.226587 40.474256 29 2459289 5100187 35.21408 40.464851 30 742573 38465 35.226452 40.473085 31 2322598 796212 35.213882 40.462839 32 1562690 5469877 35.203165 40.452471 33 819853 118718 35.202868 40.455691 34 2417372 2551145 35.203081 40.456371 35 2163895 3841879 35.222587 40.468909 36 101187291 2056865 35.239674 40.481615 37 0 4229645 35.244843 40.485967 38 0 346260 35.238007 40.483308 39 0 4912842 35.237426 40.479925 40 0 0 35.233614 40.476191 41 0 330374324 35.215561 40.464011 42 0 0 35.208138 40.458671 43 0 0 35.214791 40.463891 44 0 0 35.220713 40.467208 45 0 0 35.219622 40.465106 46 0 0 35.213646 40.460853 47 0 0 35.206988 40.457379 48 0 0 35.193229 40.446697 49 0 0 35.17646 40.435117 50 0 0 35.176039 40.434526 51 0 0 35.164066 40.427169 52 0 0 35.13442 40.40602 53 0 0 35.104214 40.385655 54 0 0 35.102211 40.381658 55 0 0 35.066148 40.354248 56 0 0 35.022438 40.324766 57 0 0 35.028433 40.327638 58 0 0 34.976069 40.287346 59 0 0 34.915728 40.244511 60 0 0 34.864939 40.212582 61 0 0 34.795481 40.157925 62 0 0 34.729434 40.105176 63 0 0 34.65674 40.048452 64 0 0 34.554064 39.968705 65 0 0 34.449277 39.891939 66 0 0 34.355906 39.82313 67 0 0 34.254694 39.743105 68 0 0 34.13077 39.651811 69 0 0 33.995792 39.547156 70 0 0 33.853038 39.433787 71 0 0 33.720582 39.329048 72 0 0 33.577975 39.212314 73 0 0 33.437461 39.100507 74 0 0 33.310998 38.999306 75 0 0 33.195374 38.909334 76 0 0 33.087335 38.82349 77 0 0 32.98884 38.74893 78 0 0 32.89679 38.679101 79 0 0 32.823499 38.623247 80 0 0 32.754294 38.564339 81 0 0 32.720745 38.536526 82 0 0 32.689974 38.50621 83 0 0 32.662086 38.481141 84 0 0 32.647011 38.467917 85 0 0 32.636908 38.453054 86 0 0 32.614819 38.433549 87 0 0 32.587837 38.409557 88 0 0 32.564029 38.385504 89 0 0 32.534183 38.357795 90 0 0 32.483032 38.315687 91 0 0 32.449774 38.282671 92 0 0 32.429584 38.264852 93 0 0 32.38798 38.228468 94 0 0 32.353682 38.199296 95 0 0 32.330356 38.182412 96 0 0 32.302594 38.15681 97 0 0 32.276111 38.136276 98 0 0 32.28932 38.14672 99 0 0 32.306269 38.157337 100 0 0 32.349115 38.193804 101 0 0 32.388005 38.223328 102 0 0 32.447044 38.270219 103 0 0 32.500448 38.310215 104 0 0 32.538321 38.337955 105 0 0 32.572727 38.359975 106 0 0 32.608584 38.38389 107 0 0 32.614656 38.386156 108 0 0 32.626362 38.397088 109 0 0 32.620208 38.390287 110 0 0 32.593137 38.368242 111 0 0 32.574583 38.355749 112 0 0 32.537939 38.323086 113 0 0 32.472474 38.270181 114 0 0 32.437986 38.241628 115 0 0 32.385247 38.198881 116 0 0 32.358177 38.175722 117 0 0 32.34048 38.169861 118 0 0 32.344624 38.174376 119 0 0 32.360172 38.188392 120 0 0 32.377807 38.202299 121 0 0 32.389781 38.209085 122 0 0 32.402908 38.216422 123 0 0 32.429867 38.241894 124 0 0 32.451314 38.254589 125 0 0 32.483305 38.273969 126 0 0 32.500515 38.286107 127 0 0 32.513181 38.291634 128 0 0 32.499763 38.271993 129 0 0 32.508128 38.284101 130 0 0 32.462005 38.240897 131 0 0 32.432496 38.215114 132 0 0 32.435579 38.221942 133 0 0 32.419477 38.204841 134 0 0 32.401016 38.189133 135 0 0 32.408805 38.192294 136 0 0 32.409558 38.190043 137 0 0 32.396235 38.186577 138 0 0 32.380911 38.168707 139 0 0 32.408969 38.190432 140 0 0 32.456835 38.2324 141 0 0 32.466663 38.238331 142 0 0 32.519643 38.282115 143 0 0 32.538243 38.29502 144 0 0 32.525888 38.284557 145 0 0 32.517309 38.276978 146 0 0 32.486149 38.245465 147 0 0 32.468823 38.231742 148 0 0 32.432838 38.198946 149 0 0 32.406889 38.178054 150 0 0 32.374568 38.148526 151 0 0 32.326288 38.106478 152 0 0 32.327297 38.11117 153 0 0 32.285601 38.078196 154 0 0 32.306727 38.095999 155 0 0 32.329821 38.109989 156 0 0 32.345134 38.120196 157 0 0 32.382222 38.15238 158 0 0 32.411728 38.175616 159 0 0 32.434252 38.192399 160 0 0 32.451365 38.208205 161 0 0 32.518787 38.261509 162 0 0 32.511801 38.251783 163 0 0 32.546326 38.284346 164 0 0 32.595992 38.316886 165 0 0 32.618954 38.337549 166 0 0 32.612725 38.326604 167 0 0 32.604289 38.32032 168 0 0 32.567942 38.288688 169 0 0 32.573986 38.289707 170 0 0 32.513235 38.237114 171 0 0 32.502993 38.231782 172 0 0 32.542244 38.26873 173 0 0 32.503644 38.235825 174 0 0 32.532976 38.256072 175 0 0 32.516491 38.245971 176 0 0 32.545658 38.279896 177 0 0 32.575372 38.298624 178 0 0 32.666156 38.371362 179 0 0 32.662556 38.378767 180 0 0 32.715072 38.419387 181 0 0 32.785512 38.47765 182 0 0 32.808782 38.496595 183 0 0 32.88069 38.556016 184 0 0 32.901874 38.581259 185 0 0 32.917408 38.591991 186 0 0 32.923752 38.587768 187 0 0 32.994094 38.657703 188 0 0 32.957938 38.619513 189 0 0 33.005226 38.666793 190 0 0 32.949642 38.626899 191 0 0 32.958662 38.629644 192 0 0 32.976406 38.653737 193 0 0 32.934717 38.621048 194 0 0 32.902201 38.607608 195 0 0 32.934157 38.635021 196 0 0 32.859795 38.590857 197 0 0 32.927055 38.635706 198 0 0 32.938192 38.661154 199 0 0 32.885705 38.621648 200 0 0 32.90839 38.64948 201 0 0 32.872064 38.628564 202 0 0 32.833809 38.617461 203 0 0 32.892035 38.657535 204 0 0 32.888718 38.668561 205 0 0 32.781397 38.576957 206 0 0 32.7745 38.588077 207 0 0 32.787057 38.596688 208 0 0 32.752203 38.574783 209 0 0 32.709794 38.557168 210 0 0 32.710987 38.565867 211 0 0 32.607461 38.492368 212 0 0 32.639794 38.512123 213 0 0 32.577088 38.474685 214 0 0 32.569275 38.473196 215 0 0 32.52028 38.45297 216 0 0 32.450049 38.401524 217 0 0 32.498848 38.427841 218 0 0 32.39908 38.350465 219 0 0 32.449302 38.398641 220 0 0 32.368441 38.34465 221 0 0 32.359314 38.35977 222 0 0 32.351747 38.336683 223 0 0 32.389019 38.373884 224 0 0 32.363631 38.360155 225 0 0 32.362326 38.335999 226 0 0 32.385084 38.36325 227 0 0 32.33926 38.346545 228 0 0 32.325912 38.324778 229 0 0 32.358504 38.335148 230 0 0 32.239425 38.269618 231 0 0 32.263831 38.279152 232 0 0 32.220924 38.247158 233 0 0 32.282345 38.328489 234 0 0 32.113741 38.173039 235 0 0 32.198624 38.227262 236 0 0 32.205896 38.253898 237 0 0 32.063217 38.130656 238 0 0 32.21894 38.281935 239 0 0 32.096552 38.181363 240 0 0 32.082158 38.167301 241 0 0 31.924331 38.079278 242 0 0 31.915626 38.070392 243 0 0 31.873676 38.060262 244 0 0 31.929487 38.106968 245 0 0 31.916758 38.103393 246 0 0 31.619324 37.859292 247 0 0 31.920621 38.078354 248 0 0 31.930674 38.099869 249 0 0 31.822425 38.002628 250 0 0 31.552683 37.838678 251 0 0 31.599796 37.872935 252 0 0 31.606411 37.854791 253 0 0 31.637881 37.902576 254 0 0 31.200676 37.641927 255 0 0 31.155899 37.557769 256 0 0 31.298821 37.687454 257 0 0 31.267971 37.693581 258 0 0 31.496073 37.817661 259 0 0 31.277814 37.639274 260 0 0 31.107346 37.579334 261 0 0 31.324 37.712627 262 0 0 31.170471 37.641897 263 0 0 30.949212 37.41773 264 0 0 31.108428 37.54976 265 0 0 31.098945 37.544943 266 0 0 30.88125 37.420199 267 0 0 30.815458 37.319985 268 0 0 30.715113 37.295213 269 0 0 30.830746 37.409254 270 0 0 30.527301 37.224335 271 0 0 30.317795 37.060577 272 0 0 30.427328 37.124611 273 0 0 30.403954 37.129379 274 0 0 30.414237 37.097175 275 0 0 30.332171 37.078541 276 0 0 30.334773 37.082553 277 0 0 30.176644 36.956763 278 0 0 29.999619 36.830476 279 0 0 30.083661 36.911757 280 0 0 29.624039 36.523944 281 0 0 29.749585 36.700997 282 0 0 30.009918 36.847923 283 0 0 29.748881 36.608326 284 0 0 29.917521 36.743865 285 0 0 29.619233 36.624251 286 0 0 29.907426 36.784164 287 0 0 29.452004 36.39012 288 0 0 29.852405 36.715128 289 0 0 29.631366 36.54591 290 0 0 29.617216 36.493895 291 0 0 29.41688 36.325448 292 0 0 29.665995 36.579301 293 0 0 29.53277 36.50599 294 0 0 29.426547 36.457122 295 0 0 29.385271 36.413953 296 0 0 29.169519 36.305623 297 0 0 29.380342 36.44302 298 0 0 29.03033 36.16741 299 0 0 28.874414 36.052796 300 0 0 28.60844 35.992149 301 0 0 28.421162 35.709889 302 0 0 28.785479 36.005867 303 0 0 29.237819 36.288476 304 0 0 28.71481 36.013056 305 0 0 28.795337 35.977116 306 0 0 28.756164 35.984475 307 0 0 28.393851 35.654466 308 0 0 28.054517 35.587747 309 0 0 28.130293 35.54886 310 0 0 28.913428 36.108363 311 0 0 28.605364 35.916986 312 0 0 27.910204 35.455102 313 0 0 28.352814 35.707071 314 0 0 27.750588 35.249412 315 0 0 27.70202 35.217172 316 0 0 28.290503 35.670391 317 0 0 28.526627 35.804734 318 0 0 28.62623 35.634973 319 0 0 28.056537 35.352179 320 0 0 28.584906 35.96478 321 0 0 28.374486 35.617284 322 0 0 28.527027 35.836336 323 0 0 27.558824 35.143791 324 0 0 27.654255 35.381206 325 0 0 28.117647 35.523529 326 0 0 28.937888 36.066253 327 0 0 27.659574 35.007092 328 0 0 28.472 35.906667 329 0 0 28.230088 35.784661 330 0 0 27.041237 34.597938 331 0 0 29.111111 35.907407 332 0 0 27.357143 34.809524 333 0 0 30.909091 37.580087 334 0 0 28.285714 36.238095 335 0 0 29.188679 36.496855 336 0 0 25.382979 33.638298 337 0 0 29.139535 36.209302 338 0 0 29.166667 36.055556 339 0 0 27.225806 35.021505 340 0 0 26.965517 33.83908 341 0 0 29.166667 36.111111 342 0 0 25.1 33.55 343 0 0 28.294118 34.941176 344 0 0 29.2 36.511111 345 0 0 24.6 31.6 346 0 0 34.75 40.125 347 0 0 26.285714 33.904762 348 0 0 30.571429 37.333333 349 0 0 33.666667 38.388889 350 0 0 27.166667 35 351 0 0 29 37.388889 352 0 0 24.2 31.866667 353 0 0 23.25 32.583333 354 0 0 31.25 38.833333 355 0 0 23 32.416667 356 0 0 33.5 39.75 357 0 0 25.25 35.166667 358 0 0 17.666667 27.444444 359 0 0 29.666667 36.555556 360 0 0 31 36 361 0 0 34 39.666667 362 0 0 32.5 39 363 0 0 36 41 364 0 0 36 41 365 0 0 22 32 366 0 0 31 38 367 0 0 31 36.333333 368 0 0 17 33 369 0 0 36 41 370 0 0 36 41 371 0 0 36 41