## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5401-Z0090-CAATATGCACGTGAT/441525-L5401-Z0090-CAATATGCACGTGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5401-Z0090-CAATATGCACGTGAT/441525-L5401-Z0090-CAATATGCACGTGAT_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 02:56:37 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 1001433 1001433 125 125380595 125380595 120610604 120610604 111668335 111668335 0 0 0.961956 0.890635 0 0.961956 0.890635 0 376141785 376141785 369782333 369782333 355524103 355524103 331813285 331813285 0.983093 0.945186 0.882149 0.983093 0.945186 0.882149 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 766 0 35.993714 40.995047 1 10573 0 35.98613 40.990156 2 12926 4102 35.995146 40.995804 3 32643 1154 35.977157 40.981099 4 53574 44897 35.98991 40.991934 5 105719 16671 35.995087 40.995932 6 112633 116764 35.980485 40.983946 7 186563 148961 35.982027 40.987717 8 192200 147219 35.988795 40.990865 9 229556 104928 35.963459 40.969173 10 241397 498128 35.885196 40.92393 11 287568 58073 35.945223 40.960423 12 347455 692187 35.145679 40.280993 13 346782 204652 33.5421 39.472222 14 450751 978037 35.914936 40.948393 15 361807 370578 35.848274 40.895228 16 386297 447108 35.837439 40.856943 17 506848 1110247 35.915664 40.92816 18 542758 709992 35.66971 40.724039 19 361175 705754 35.71052 40.781594 20 490221 997498 35.906009 40.937906 21 642808 1313877 35.846952 40.891156 22 310975 559362 35.619298 40.739075 23 1006888 1166449 35.338349 40.548123 24 562950 1126688 35.328943 40.545628 25 531781 463227 35.324951 40.541541 26 1698185 2472839 35.257587 40.492892 27 344840 822756 35.267094 40.500978 28 943845 364133 35.290223 40.518454 29 2409776 4971401 35.284577 40.513719 30 715239 40689 35.275477 40.506746 31 2246042 753761 35.267999 40.499684 32 1552068 5333684 35.257303 40.492692 33 788860 119162 35.255175 40.490387 34 2358674 2499516 35.24562 40.484837 35 2096277 3727359 35.264665 40.4962 36 101911175 2002677 35.287633 40.51352 37 0 4104910 35.284675 40.51229 38 0 346523 35.276135 40.507158 39 0 4782537 35.277981 40.506093 40 0 0 35.27307 40.503156 41 0 331813285 35.262361 40.495568 42 0 0 35.250781 40.487435 43 0 0 35.258138 40.491255 44 0 0 35.265432 40.497063 45 0 0 35.266679 40.498125 46 0 0 35.247477 40.485155 47 0 0 35.238565 40.478048 48 0 0 35.231049 40.472 49 0 0 35.223742 40.466507 50 0 0 35.216312 40.462036 51 0 0 35.204501 40.453837 52 0 0 35.19735 40.449257 53 0 0 35.183539 40.438855 54 0 0 35.170379 40.429163 55 0 0 35.143526 40.410149 56 0 0 35.12168 40.394375 57 0 0 35.087701 40.369257 58 0 0 35.058191 40.34856 59 0 0 35.00567 40.309842 60 0 0 34.956418 40.274056 61 0 0 34.898612 40.228703 62 0 0 34.8243 40.17291 63 0 0 34.756179 40.122917 64 0 0 34.670334 40.054815 65 0 0 34.577666 39.985695 66 0 0 34.472631 39.908012 67 0 0 34.365789 39.830313 68 0 0 34.254653 39.744642 69 0 0 34.118123 39.63917 70 0 0 33.99548 39.542594 71 0 0 33.855807 39.427592 72 0 0 33.716399 39.313551 73 0 0 33.581005 39.205879 74 0 0 33.45163 39.105101 75 0 0 33.329781 39.006541 76 0 0 33.215723 38.921419 77 0 0 33.113429 38.847717 78 0 0 33.011511 38.766511 79 0 0 32.927981 38.697631 80 0 0 32.864456 38.64417 81 0 0 32.80914 38.598492 82 0 0 32.754622 38.551055 83 0 0 32.724505 38.523578 84 0 0 32.70108 38.501734 85 0 0 32.676463 38.48362 86 0 0 32.655048 38.463233 87 0 0 32.61932 38.430457 88 0 0 32.575413 38.393438 89 0 0 32.54344 38.360986 90 0 0 32.499476 38.32382 91 0 0 32.475659 38.299422 92 0 0 32.442052 38.269292 93 0 0 32.403751 38.23557 94 0 0 32.358518 38.199594 95 0 0 32.341697 38.186602 96 0 0 32.32088 38.166811 97 0 0 32.287684 38.14136 98 0 0 32.303444 38.154531 99 0 0 32.340231 38.184359 100 0 0 32.390849 38.221801 101 0 0 32.441482 38.259284 102 0 0 32.492902 38.301357 103 0 0 32.541676 38.335502 104 0 0 32.58113 38.364328 105 0 0 32.613226 38.38682 106 0 0 32.649048 38.411621 107 0 0 32.654823 38.411601 108 0 0 32.652784 38.41206 109 0 0 32.639797 38.403958 110 0 0 32.6423 38.402728 111 0 0 32.610258 38.377159 112 0 0 32.564162 38.335298 113 0 0 32.511955 38.297874 114 0 0 32.473338 38.264476 115 0 0 32.440689 38.237831 116 0 0 32.402457 38.209427 117 0 0 32.410055 38.220816 118 0 0 32.408946 38.223486 119 0 0 32.421951 38.231721 120 0 0 32.444612 38.253302 121 0 0 32.467459 38.269489 122 0 0 32.478735 38.273418 123 0 0 32.504878 38.299159 124 0 0 32.520149 38.30382 125 0 0 32.553079 38.324981 126 0 0 32.586003 38.350162 127 0 0 32.571363 38.32827 128 0 0 32.586445 38.337734 129 0 0 32.545605 38.303565 130 0 0 32.531267 38.291327 131 0 0 32.519862 38.278324 132 0 0 32.511344 38.272305 133 0 0 32.501691 38.266748 134 0 0 32.502004 38.264398 135 0 0 32.509452 38.269881 136 0 0 32.493235 38.254984 137 0 0 32.498602 38.259363 138 0 0 32.490346 38.255203 139 0 0 32.545767 38.299706 140 0 0 32.556033 38.30709 141 0 0 32.578343 38.327212 142 0 0 32.597562 38.339022 143 0 0 32.606254 38.344708 144 0 0 32.588772 38.330557 145 0 0 32.585324 38.319977 146 0 0 32.554368 38.297751 147 0 0 32.556025 38.293103 148 0 0 32.546546 38.283432 149 0 0 32.496732 38.241824 150 0 0 32.469754 38.224139 151 0 0 32.402173 38.164683 152 0 0 32.384696 38.153408 153 0 0 32.413043 38.173879 154 0 0 32.387025 38.151501 155 0 0 32.407919 38.168192 156 0 0 32.445282 38.199726 157 0 0 32.471887 38.224104 158 0 0 32.518345 38.253068 159 0 0 32.544308 38.27836 160 0 0 32.5754 38.299757 161 0 0 32.576474 38.304783 162 0 0 32.624465 38.34043 163 0 0 32.663318 38.376684 164 0 0 32.670589 38.380904 165 0 0 32.684367 38.388114 166 0 0 32.687729 38.386784 167 0 0 32.670412 38.377099 168 0 0 32.617316 38.321695 169 0 0 32.606902 38.3197 170 0 0 32.591833 38.294766 171 0 0 32.558742 38.265079 172 0 0 32.55801 38.275919 173 0 0 32.581887 38.297841 174 0 0 32.585013 38.293501 175 0 0 32.626275 38.340028 176 0 0 32.642207 38.343473 177 0 0 32.705367 38.403058 178 0 0 32.740053 38.432923 179 0 0 32.791905 38.467363 180 0 0 32.852527 38.531182 181 0 0 32.872553 38.542697 182 0 0 32.926403 38.586779 183 0 0 32.936426 38.604167 184 0 0 32.98338 38.632739 185 0 0 33.038923 38.68257 186 0 0 33.054743 38.695276 187 0 0 33.083668 38.72481 188 0 0 33.100915 38.738979 189 0 0 33.158939 38.776809 190 0 0 33.100349 38.735518 191 0 0 33.10138 38.736986 192 0 0 33.077316 38.728396 193 0 0 33.033946 38.697951 194 0 0 33.039812 38.709715 195 0 0 33.047853 38.716513 196 0 0 32.994145 38.684591 197 0 0 33.040275 38.723007 198 0 0 33.035879 38.731486 199 0 0 33.03124 38.727701 200 0 0 33.003246 38.715729 201 0 0 32.990081 38.717453 202 0 0 33.048038 38.761867 203 0 0 32.97676 38.714489 204 0 0 32.990523 38.737545 205 0 0 33.000862 38.747361 206 0 0 32.965802 38.729113 207 0 0 32.937453 38.698732 208 0 0 32.915091 38.69031 209 0 0 32.878292 38.658293 210 0 0 32.878179 38.677683 211 0 0 32.901121 38.693922 212 0 0 32.83796 38.656681 213 0 0 32.853557 38.659818 214 0 0 32.857078 38.671892 215 0 0 32.787586 38.635766 216 0 0 32.731607 38.591044 217 0 0 32.740982 38.594175 218 0 0 32.761343 38.613321 219 0 0 32.694426 38.568883 220 0 0 32.717655 38.588262 221 0 0 32.65306 38.539259 222 0 0 32.681718 38.57101 223 0 0 32.653983 38.54664 224 0 0 32.670786 38.547524 225 0 0 32.56292 38.490114 226 0 0 32.565938 38.493637 227 0 0 32.569487 38.511888 228 0 0 32.4507 38.425988 229 0 0 32.425954 38.375175 230 0 0 32.464639 38.428266 231 0 0 32.374722 38.374281 232 0 0 32.376457 38.368833 233 0 0 32.427388 38.401954 234 0 0 32.256477 38.288943 235 0 0 32.337774 38.348159 236 0 0 32.374919 38.373166 237 0 0 32.304416 38.32616 238 0 0 32.189026 38.260585 239 0 0 32.2111 38.267291 240 0 0 32.204683 38.288688 241 0 0 32.089924 38.197215 242 0 0 32.192792 38.263921 243 0 0 32.06308 38.184893 244 0 0 32.14666 38.227854 245 0 0 31.890195 38.075358 246 0 0 32.001522 38.155643 247 0 0 31.88338 38.050448 248 0 0 31.907686 38.102007 249 0 0 31.968715 38.11131 250 0 0 31.826127 38.038844 251 0 0 31.898008 38.073959 252 0 0 31.761313 37.996557 253 0 0 31.792405 38.010338 254 0 0 31.794919 38.028969 255 0 0 31.803002 38.024792 256 0 0 31.592526 37.87677 257 0 0 31.666572 37.954634 258 0 0 31.468786 37.813643 259 0 0 31.486983 37.805468 260 0 0 31.45543 37.809001 261 0 0 31.280992 37.688917 262 0 0 31.309438 37.717505 263 0 0 31.133915 37.547743 264 0 0 31.197246 37.632014 265 0 0 31.141544 37.592154 266 0 0 31.042159 37.546005 267 0 0 30.97259 37.524147 268 0 0 31.140491 37.610064 269 0 0 30.872908 37.45556 270 0 0 30.917628 37.452978 271 0 0 30.791997 37.332724 272 0 0 30.927231 37.465318 273 0 0 30.743151 37.29024 274 0 0 30.79194 37.387283 275 0 0 30.540649 37.148563 276 0 0 30.486016 37.136864 277 0 0 30.583882 37.237312 278 0 0 30.339754 37.091179 279 0 0 30.139247 36.948216 280 0 0 30.255081 36.988482 281 0 0 30.097027 36.932968 282 0 0 29.989831 36.869414 283 0 0 29.827049 36.736612 284 0 0 29.928088 36.713856 285 0 0 30.044225 36.889729 286 0 0 30.020078 36.886125 287 0 0 29.839098 36.721227 288 0 0 29.624403 36.581714 289 0 0 29.393151 36.401163 290 0 0 29.330842 36.367754 291 0 0 29.283907 36.3078 292 0 0 29.509496 36.534819 293 0 0 29.400528 36.350917 294 0 0 29.46091 36.410865 295 0 0 29.186923 36.283059 296 0 0 29.128924 36.302498 297 0 0 28.920296 35.999274 298 0 0 28.890725 36.097949 299 0 0 28.904945 36.057129 300 0 0 29.015083 36.075918 301 0 0 28.591125 35.855432 302 0 0 28.824018 36.015311 303 0 0 28.502627 35.81475 304 0 0 29.029666 36.180264 305 0 0 28.623529 35.820915 306 0 0 28.594744 35.913555 307 0 0 28.42117 35.605477 308 0 0 28.249012 35.645323 309 0 0 28.7225 35.999722 310 0 0 28.329137 35.71193 311 0 0 28.625 36.022756 312 0 0 28.296715 35.634839 313 0 0 28.48427 35.90824 314 0 0 28.666667 35.948656 315 0 0 27.969231 35.421795 316 0 0 28.273232 35.609339 317 0 0 28.440729 35.766971 318 0 0 28.026446 35.46832 319 0 0 28.452594 35.677996 320 0 0 28.449799 35.797858 321 0 0 28.415138 35.620031 322 0 0 28.835897 36.037607 323 0 0 27.322857 34.766667 324 0 0 28.109422 35.693009 325 0 0 28.206081 35.622748 326 0 0 28.736059 36.08798 327 0 0 28.46748 35.868564 328 0 0 27.556522 34.888406 329 0 0 27.733333 35.457143 330 0 0 27.989189 35.542342 331 0 0 28.140351 35.385965 332 0 0 27.316129 35.208602 333 0 0 26 34.217284 334 0 0 25.958333 33.855556 335 0 0 27.66055 35.076453 336 0 0 28.406593 35.578755 337 0 0 27.148148 34.193416 338 0 0 27.712329 35.401826 339 0 0 28.610169 36.073446 340 0 0 25.615385 33.108974 341 0 0 28.0625 35.777778 342 0 0 27.358974 34.760684 343 0 0 27.714286 35.038095 344 0 0 27.676471 35.519608 345 0 0 26.423077 33.948718 346 0 0 28.086957 35.275362 347 0 0 28 34.941176 348 0 0 24.615385 32.461538 349 0 0 24.833333 33.055556 350 0 0 28.9 35.966667 351 0 0 22 30.428571 352 0 0 27.8 35.866667 353 0 0 26.333333 34.777778 354 0 0 35.5 40.333333 355 0 0 35.5 40.333333 356 0 0 35 40 357 0 0 33.5 39.5 358 0 0 33 38.5 359 0 0 5 12.333333 360 0 0 23 33 361 0 0 26 35.333333 362 0 0 26 36 363 0 0 36 41 364 0 0 26 36 365 0 0 8 30 366 0 0 15 27.666667 367 0 0 32 38.666667 368 0 0 23 35