## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5390-Z0076-CACAATGTGCGCGAT/441525-L5390-Z0076-CACAATGTGCGCGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5390-Z0076-CACAATGTGCGCGAT/441525-L5390-Z0076-CACAATGTGCGCGAT_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 02:54:30 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 1001180 1001180 137 137734470 137734470 132837795 132837795 123485695 123485695 0 0 0.964448 0.896549 0 0.964448 0.896549 0 413203410 413203410 406752656 406752656 391778644 391778644 366560013 366560013 0.984388 0.94815 0.887118 0.984388 0.94815 0.887118 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 854 0 35.992509 40.994189 1 11281 1 35.985439 40.989624 2 13765 4352 35.993743 40.994774 3 33857 1264 35.979288 40.98306 4 55278 47944 35.989348 40.991355 5 111003 17409 35.994326 40.995213 6 109974 124793 35.979883 40.983454 7 196693 159095 35.979285 40.98601 8 195099 149511 35.987999 40.989966 9 242198 110189 35.955755 40.962702 10 250608 510030 35.848303 40.90696 11 295195 61988 35.90771 40.931968 12 348942 712209 35.097449 40.246126 13 352636 199592 33.431756 39.416061 14 455340 987031 35.866593 40.917262 15 372915 372826 35.836189 40.883376 16 383659 430089 35.808624 40.830449 17 523967 1108775 35.917058 40.930753 18 555561 738141 35.728366 40.778965 19 387850 715515 35.753211 40.820728 20 519926 1013497 35.909553 40.939633 21 689095 1409990 35.826084 40.8762 22 336651 569874 35.602085 40.733535 23 1054064 1253945 35.322844 40.547899 24 607225 1234406 35.344761 40.5603 25 554532 500199 35.32182 40.544195 26 1764838 2533549 35.272305 40.506762 27 374608 901307 35.285768 40.517749 28 977183 417005 35.310757 40.534834 29 2473978 5140240 35.310504 40.533829 30 796915 42188 35.292396 40.520005 31 2416696 860636 35.288002 40.515836 32 1675987 5502246 35.299884 40.522598 33 868799 128130 35.289931 40.517216 34 2519792 2805921 35.286786 40.514934 35 2272887 3867986 35.302755 40.524768 36 112934619 2204070 35.321375 40.53855 37 0 4297287 35.326378 40.542728 38 0 394655 35.312971 40.532868 39 0 5115512 35.317082 40.536505 40 0 0 35.307422 40.529155 41 0 366560013 35.294912 40.519968 42 0 0 35.288188 40.515302 43 0 0 35.294192 40.518896 44 0 0 35.302322 40.525339 45 0 0 35.302692 40.525246 46 0 0 35.29669 40.519826 47 0 0 35.287657 40.513961 48 0 0 35.275598 40.507049 49 0 0 35.272914 40.504612 50 0 0 35.268092 40.50042 51 0 0 35.264809 40.498642 52 0 0 35.257469 40.492526 53 0 0 35.24342 40.483874 54 0 0 35.245055 40.483888 55 0 0 35.229783 40.472399 56 0 0 35.216764 40.463266 57 0 0 35.202079 40.453465 58 0 0 35.18565 40.441528 59 0 0 35.156037 40.419034 60 0 0 35.1305 40.400552 61 0 0 35.095138 40.374478 62 0 0 35.062104 40.348805 63 0 0 35.020264 40.316488 64 0 0 34.96901 40.280119 65 0 0 34.921228 40.244042 66 0 0 34.862698 40.200481 67 0 0 34.798026 40.153187 68 0 0 34.72565 40.100753 69 0 0 34.643456 40.037717 70 0 0 34.55896 39.971783 71 0 0 34.474883 39.902716 72 0 0 34.374804 39.822868 73 0 0 34.277554 39.746076 74 0 0 34.181133 39.668475 75 0 0 34.07963 39.590999 76 0 0 33.987495 39.517984 77 0 0 33.896674 39.450711 78 0 0 33.798537 39.373515 79 0 0 33.722487 39.31523 80 0 0 33.640068 39.247745 81 0 0 33.577331 39.197325 82 0 0 33.512179 39.141946 83 0 0 33.447996 39.090703 84 0 0 33.403682 39.05555 85 0 0 33.360155 39.02034 86 0 0 33.314507 38.981812 87 0 0 33.270145 38.948352 88 0 0 33.228465 38.909981 89 0 0 33.178985 38.868676 90 0 0 33.134556 38.830821 91 0 0 33.087902 38.787049 92 0 0 33.057234 38.759826 93 0 0 33.028958 38.735741 94 0 0 32.989256 38.700566 95 0 0 32.967545 38.683113 96 0 0 32.947608 38.665798 97 0 0 32.933541 38.651828 98 0 0 32.929029 38.648062 99 0 0 32.948653 38.661405 100 0 0 32.963343 38.67404 101 0 0 33.01188 38.711816 102 0 0 33.03968 38.732839 103 0 0 33.063755 38.750989 104 0 0 33.077036 38.75727 105 0 0 33.08994 38.766496 106 0 0 33.08715 38.758786 107 0 0 33.077642 38.752011 108 0 0 33.060876 38.73912 109 0 0 33.046279 38.724803 110 0 0 33.012609 38.699512 111 0 0 32.977385 38.671315 112 0 0 32.916398 38.618397 113 0 0 32.85126 38.567714 114 0 0 32.796878 38.518588 115 0 0 32.734913 38.473702 116 0 0 32.694893 38.441162 117 0 0 32.676871 38.429609 118 0 0 32.677557 38.432261 119 0 0 32.677035 38.431983 120 0 0 32.684165 38.444627 121 0 0 32.697015 38.448617 122 0 0 32.710705 38.460036 123 0 0 32.722323 38.468373 124 0 0 32.740382 38.477227 125 0 0 32.754709 38.485724 126 0 0 32.762955 38.490261 127 0 0 32.744834 38.470233 128 0 0 32.727719 38.452936 129 0 0 32.720413 38.441569 130 0 0 32.681399 38.411966 131 0 0 32.665716 38.400407 132 0 0 32.641727 38.377755 133 0 0 32.634131 38.372611 134 0 0 32.635227 38.370941 135 0 0 32.613316 38.350722 136 0 0 32.627165 38.358524 137 0 0 32.609668 38.3432 138 0 0 32.604929 38.344616 139 0 0 32.633508 38.371732 140 0 0 32.663165 38.391256 141 0 0 32.682011 38.411201 142 0 0 32.701261 38.429797 143 0 0 32.708202 38.427099 144 0 0 32.726611 38.441059 145 0 0 32.684875 38.401317 146 0 0 32.663809 38.384026 147 0 0 32.622707 38.34965 148 0 0 32.603041 38.328007 149 0 0 32.58068 38.309737 150 0 0 32.551259 38.283478 151 0 0 32.502425 38.246842 152 0 0 32.476618 38.228529 153 0 0 32.456078 38.21219 154 0 0 32.45275 38.213277 155 0 0 32.471601 38.2304 156 0 0 32.501805 38.247614 157 0 0 32.536454 38.278818 158 0 0 32.569821 38.301412 159 0 0 32.61257 38.335168 160 0 0 32.637782 38.35335 161 0 0 32.682014 38.385587 162 0 0 32.731856 38.427221 163 0 0 32.740764 38.437375 164 0 0 32.757192 38.454009 165 0 0 32.764892 38.460077 166 0 0 32.751873 38.447385 167 0 0 32.742935 38.431201 168 0 0 32.693351 38.38985 169 0 0 32.657906 38.358832 170 0 0 32.616801 38.323857 171 0 0 32.595383 38.304883 172 0 0 32.607272 38.316313 173 0 0 32.597131 38.312974 174 0 0 32.616505 38.330342 175 0 0 32.655142 38.368866 176 0 0 32.666571 38.378587 177 0 0 32.732549 38.428874 178 0 0 32.787968 38.475878 179 0 0 32.818432 38.499168 180 0 0 32.860463 38.532136 181 0 0 32.91976 38.59155 182 0 0 32.949073 38.614173 183 0 0 33.011737 38.665131 184 0 0 33.039983 38.694972 185 0 0 33.082501 38.724698 186 0 0 33.104333 38.747978 187 0 0 33.132404 38.766816 188 0 0 33.118979 38.758958 189 0 0 33.135617 38.773617 190 0 0 33.130921 38.773033 191 0 0 33.10735 38.75495 192 0 0 33.088063 38.739275 193 0 0 33.055232 38.725386 194 0 0 32.9898 38.680137 195 0 0 32.988156 38.686265 196 0 0 32.978359 38.690488 197 0 0 33.007674 38.7112 198 0 0 33.001365 38.709988 199 0 0 33.000194 38.724811 200 0 0 32.976743 38.704704 201 0 0 32.991327 38.734504 202 0 0 32.949379 38.703083 203 0 0 32.918126 38.687818 204 0 0 32.913549 38.697979 205 0 0 32.927212 38.709921 206 0 0 32.898751 38.69262 207 0 0 32.853445 38.66901 208 0 0 32.852134 38.67053 209 0 0 32.854987 38.674322 210 0 0 32.845257 38.668373 211 0 0 32.809279 38.64683 212 0 0 32.710908 38.573217 213 0 0 32.71526 38.5818 214 0 0 32.715862 38.583052 215 0 0 32.678621 38.558566 216 0 0 32.685713 38.573363 217 0 0 32.636006 38.534431 218 0 0 32.639184 38.537761 219 0 0 32.581996 38.488537 220 0 0 32.593409 38.517102 221 0 0 32.602023 38.516013 222 0 0 32.585852 38.501702 223 0 0 32.505195 38.451385 224 0 0 32.547974 38.478652 225 0 0 32.456495 38.420288 226 0 0 32.464681 38.432228 227 0 0 32.468217 38.423591 228 0 0 32.472651 38.450514 229 0 0 32.402041 38.390409 230 0 0 32.359403 38.369831 231 0 0 32.402794 38.392121 232 0 0 32.417845 38.409292 233 0 0 32.379878 38.379433 234 0 0 32.265296 38.318423 235 0 0 32.307025 38.343093 236 0 0 32.258801 38.320903 237 0 0 32.348506 38.369596 238 0 0 32.225342 38.282467 239 0 0 32.204087 38.279612 240 0 0 32.155007 38.255571 241 0 0 32.063443 38.174647 242 0 0 32.16324 38.262629 243 0 0 32.051649 38.17743 244 0 0 32.014033 38.135165 245 0 0 32.023342 38.173401 246 0 0 32.042367 38.16509 247 0 0 32.054794 38.196289 248 0 0 31.979027 38.134239 249 0 0 32.01083 38.164264 250 0 0 31.929526 38.109456 251 0 0 31.884925 38.084792 252 0 0 31.706442 37.93921 253 0 0 31.601607 37.888418 254 0 0 31.670581 37.950907 255 0 0 31.544281 37.837433 256 0 0 31.689695 37.958786 257 0 0 31.555688 37.853744 258 0 0 31.521332 37.856159 259 0 0 31.513214 37.84599 260 0 0 31.556592 37.861736 261 0 0 31.322662 37.70044 262 0 0 31.42151 37.790769 263 0 0 31.527317 37.867146 264 0 0 31.394371 37.776076 265 0 0 31.357483 37.757605 266 0 0 31.363932 37.77076 267 0 0 31.128103 37.548503 268 0 0 31.125148 37.591587 269 0 0 30.988352 37.496229 270 0 0 31.108508 37.58492 271 0 0 30.845398 37.405116 272 0 0 30.805088 37.351253 273 0 0 30.864921 37.38042 274 0 0 30.60433 37.244087 275 0 0 30.544018 37.269939 276 0 0 30.53628 37.183252 277 0 0 30.288619 37.031322 278 0 0 30.316056 37.047308 279 0 0 30.17265 36.978182 280 0 0 30.137442 36.898412 281 0 0 30.089907 36.902688 282 0 0 30.060269 36.881973 283 0 0 29.898727 36.746541 284 0 0 29.966262 36.833523 285 0 0 29.731069 36.643573 286 0 0 29.908434 36.802544 287 0 0 29.845282 36.715836 288 0 0 29.623836 36.554968 289 0 0 29.452496 36.481392 290 0 0 29.427575 36.431099 291 0 0 29.26268 36.284008 292 0 0 29.356694 36.413888 293 0 0 29.495365 36.501712 294 0 0 29.112614 36.194885 295 0 0 29.04798 36.200596 296 0 0 29.294283 36.32404 297 0 0 28.829304 36.069182 298 0 0 29.126001 36.222222 299 0 0 28.848612 35.970734 300 0 0 28.642785 35.891855 301 0 0 28.62531 35.818504 302 0 0 28.788727 35.97723 303 0 0 28.523641 35.795377 304 0 0 28.422918 35.763809 305 0 0 28.481417 35.83705 306 0 0 28.273103 35.747739 307 0 0 28.060223 35.512547 308 0 0 28.192029 35.524327 309 0 0 28.377852 35.744203 310 0 0 28.190363 35.552846 311 0 0 28.012227 35.502789 312 0 0 28.098134 35.495278 313 0 0 28.320237 35.711391 314 0 0 28.427881 35.705614 315 0 0 27.684028 35.239294 316 0 0 28.099905 35.542658 317 0 0 28.493711 35.839972 318 0 0 27.975723 35.349518 319 0 0 28.022989 35.331205 320 0 0 28.679219 35.817294 321 0 0 28.21517 35.581527 322 0 0 27.589655 35.014943 323 0 0 28.09542 35.312977 324 0 0 28.341826 35.542109 325 0 0 28.624113 35.937746 326 0 0 28.177898 35.583109 327 0 0 27.769697 35.050505 328 0 0 27.294915 35.027119 329 0 0 28.43346 35.789607 330 0 0 26.806723 34.739496 331 0 0 28.229268 35.430894 332 0 0 28.858696 35.786232 333 0 0 28.792683 36.256098 334 0 0 27.176871 34.777778 335 0 0 26.859259 34.469136 336 0 0 28.205128 35.051282 337 0 0 26.363636 33.933333 338 0 0 27.553191 35.365248 339 0 0 28.855422 36.044177 340 0 0 27.226667 35.151111 341 0 0 28.584615 35.907692 342 0 0 27.263158 35.292398 343 0 0 28.5 36.307692 344 0 0 26.15 34.1 345 0 0 25.235294 33.127451 346 0 0 30.033333 36.422222 347 0 0 27.913043 35.028986 348 0 0 29.111111 36.277778 349 0 0 25 33.2 350 0 0 31.357143 38.095238 351 0 0 29.166667 36.194444 352 0 0 24.181818 34.242424 353 0 0 27 33.714286 354 0 0 30.857143 37.761905 355 0 0 21.6 30 356 0 0 24 30.866667 357 0 0 25.6 32.8 358 0 0 30 36.866667 359 0 0 27.4 35.4 360 0 0 26.5 35.25 361 0 0 29 35 362 0 0 23.75 32.833333 363 0 0 31.5 37.75 364 0 0 19 33.666667 365 0 0 31.5 37.666667 366 0 0 30 37.166667 367 0 0 26 36 368 0 0 11 25.333333 369 0 0 17 33 370 0 0 31 38 371 0 0 36 41 372 0 0 36 41