## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5391-Z0077-CAATGACTATCTGAT/441525-L5391-Z0077-CAATGACTATCTGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5391-Z0077-CAATGACTATCTGAT/441525-L5391-Z0077-CAATGACTATCTGAT_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 02:54:25 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 1000978 1000978 113 113637854 113637854 108757914 108757914 99765712 99765712 0 0 0.957057 0.877927 0 0.957057 0.877927 0 340913562 340913562 334337964 334337964 320045219 320045219 296827347 296827347 0.980712 0.938787 0.870682 0.980712 0.938787 0.870682 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 862 0 35.994908 40.996157 1 10409 2 35.989116 40.992583 2 13061 3813 35.99505 40.995765 3 32759 1078 35.983811 40.98666 4 54814 45036 35.992049 40.993642 5 106839 18646 35.994893 40.995768 6 116965 117496 35.974585 40.978236 7 191077 157104 35.976877 40.984116 8 208048 147926 35.988692 40.990871 9 237816 110333 35.962994 40.96899 10 257869 514118 35.881003 40.927198 11 301074 60586 35.929939 40.948627 12 357327 720428 35.115584 40.251006 13 355010 222597 33.375518 39.370774 14 462376 1018668 35.897946 40.938227 15 371923 382767 35.849256 40.893786 16 387582 479391 35.83325 40.852365 17 510231 1131225 35.913566 40.926945 18 548957 738291 35.746452 40.789706 19 354941 706093 35.720835 40.791865 20 491042 1003490 35.882771 40.92401 21 656100 1330082 35.814049 40.868639 22 302744 549345 35.504623 40.668848 23 1014481 1168375 35.125697 40.408246 24 556013 1116018 35.127513 40.414607 25 527106 443406 35.156068 40.437064 26 1729549 2507214 35.070875 40.370297 27 341391 795698 35.097931 40.389882 28 931268 361426 35.135993 40.414298 29 2442508 5017691 35.144567 40.420812 30 698779 37631 35.138254 40.413411 31 2234881 715616 35.13572 40.409375 32 1490800 5355399 35.136497 40.407417 33 784638 118598 35.129725 40.405728 34 2310727 2419495 35.123677 40.400723 35 2006510 3688303 35.143074 40.413709 36 90239377 1966686 35.169466 40.43237 37 0 4004159 35.178871 40.439903 38 0 303678 35.17704 40.439296 39 0 4608307 35.166934 40.430315 40 0 0 35.158244 40.42448 41 0 296827347 35.148438 40.417792 42 0 0 35.146912 40.415404 43 0 0 35.150831 40.419116 44 0 0 35.159743 40.425958 45 0 0 35.162391 40.426434 46 0 0 35.145351 40.415366 47 0 0 35.137669 40.409168 48 0 0 35.125457 40.399084 49 0 0 35.120518 40.396775 50 0 0 35.105809 40.386812 51 0 0 35.088974 40.37475 52 0 0 35.068716 40.360815 53 0 0 35.050748 40.34849 54 0 0 35.033532 40.335199 55 0 0 34.994938 40.30886 56 0 0 34.955049 40.280181 57 0 0 34.904779 40.243029 58 0 0 34.843946 40.197627 59 0 0 34.772237 40.145557 60 0 0 34.684799 40.081524 61 0 0 34.578972 40.000656 62 0 0 34.459805 39.912015 63 0 0 34.334521 39.813535 64 0 0 34.201323 39.713155 65 0 0 34.051136 39.600909 66 0 0 33.894878 39.48403 67 0 0 33.729718 39.356009 68 0 0 33.553324 39.223551 69 0 0 33.381082 39.084711 70 0 0 33.189247 38.935514 71 0 0 33.019784 38.799397 72 0 0 32.855365 38.666038 73 0 0 32.697518 38.539185 74 0 0 32.55454 38.423318 75 0 0 32.43093 38.327184 76 0 0 32.327707 38.244703 77 0 0 32.243341 38.178435 78 0 0 32.176966 38.126861 79 0 0 32.109294 38.068529 80 0 0 32.061873 38.028805 81 0 0 32.035762 38.002791 82 0 0 32.006012 37.973371 83 0 0 31.995396 37.960994 84 0 0 31.974556 37.943972 85 0 0 31.942181 37.912357 86 0 0 31.908901 37.880012 87 0 0 31.891139 37.861556 88 0 0 31.840239 37.815041 89 0 0 31.789998 37.772702 90 0 0 31.763166 37.74651 91 0 0 31.722017 37.707774 92 0 0 31.700239 37.688262 93 0 0 31.670323 37.662637 94 0 0 31.633584 37.631393 95 0 0 31.640312 37.637286 96 0 0 31.650887 37.643472 97 0 0 31.667901 37.65732 98 0 0 31.694237 37.678646 99 0 0 31.754745 37.722605 100 0 0 31.810553 37.76643 101 0 0 31.869866 37.813114 102 0 0 31.93587 37.86654 103 0 0 31.991178 37.90465 104 0 0 32.00556 37.912781 105 0 0 32.02833 37.928649 106 0 0 32.023817 37.918016 107 0 0 31.991557 37.893911 108 0 0 31.968319 37.874139 109 0 0 31.904953 37.81861 110 0 0 31.859629 37.78585 111 0 0 31.772789 37.714447 112 0 0 31.737771 37.691712 113 0 0 31.68277 37.6466 114 0 0 31.592038 37.576125 115 0 0 31.547209 37.541542 116 0 0 31.520414 37.52295 117 0 0 31.519291 37.521069 118 0 0 31.530997 37.531432 119 0 0 31.561663 37.549019 120 0 0 31.569103 37.554166 121 0 0 31.609651 37.587244 122 0 0 31.618653 37.594132 123 0 0 31.660656 37.626523 124 0 0 31.700565 37.651944 125 0 0 31.727512 37.67237 126 0 0 31.727511 37.667862 127 0 0 31.751761 37.679894 128 0 0 31.728547 37.656036 129 0 0 31.697411 37.625042 130 0 0 31.633926 37.572584 131 0 0 31.604277 37.551591 132 0 0 31.619144 37.563494 133 0 0 31.655364 37.592826 134 0 0 31.646218 37.581311 135 0 0 31.619855 37.559122 136 0 0 31.64551 37.58106 137 0 0 31.662692 37.595002 138 0 0 31.703753 37.62854 139 0 0 31.752536 37.669102 140 0 0 31.753808 37.673946 141 0 0 31.806511 37.717429 142 0 0 31.820426 37.725954 143 0 0 31.86687 37.763851 144 0 0 31.870483 37.766173 145 0 0 31.834955 37.727977 146 0 0 31.862124 37.757938 147 0 0 31.833596 37.722628 148 0 0 31.820721 37.7115 149 0 0 31.813556 37.702478 150 0 0 31.770994 37.664689 151 0 0 31.747886 37.65418 152 0 0 31.721232 37.631219 153 0 0 31.747362 37.647052 154 0 0 31.761554 37.672871 155 0 0 31.783842 37.690408 156 0 0 31.807462 37.697146 157 0 0 31.877114 37.766942 158 0 0 31.939255 37.810383 159 0 0 32.026486 37.875324 160 0 0 32.034197 37.883603 161 0 0 32.082847 37.918178 162 0 0 32.154512 37.980888 163 0 0 32.224644 38.039566 164 0 0 32.249212 38.053432 165 0 0 32.289908 38.088465 166 0 0 32.298239 38.090713 167 0 0 32.3434 38.126358 168 0 0 32.337782 38.117341 169 0 0 32.361871 38.142697 170 0 0 32.317105 38.093217 171 0 0 32.366906 38.137058 172 0 0 32.362377 38.134305 173 0 0 32.401018 38.168042 174 0 0 32.430376 38.18504 175 0 0 32.377724 38.159307 176 0 0 32.420706 38.202299 177 0 0 32.490193 38.261907 178 0 0 32.506001 38.285699 179 0 0 32.568279 38.318318 180 0 0 32.632193 38.381864 181 0 0 32.641447 38.386184 182 0 0 32.72126 38.453117 183 0 0 32.760911 38.483614 184 0 0 32.783112 38.492142 185 0 0 32.803243 38.517264 186 0 0 32.765205 38.498198 187 0 0 32.858388 38.549166 188 0 0 32.963485 38.661193 189 0 0 32.955184 38.663938 190 0 0 32.907414 38.619508 191 0 0 32.96506 38.652783 192 0 0 32.939305 38.646004 193 0 0 32.924016 38.641431 194 0 0 32.916659 38.634968 195 0 0 32.958613 38.67422 196 0 0 32.949638 38.678951 197 0 0 32.825195 38.604226 198 0 0 32.891015 38.654824 199 0 0 32.839396 38.616486 200 0 0 32.931878 38.694925 201 0 0 32.992745 38.752387 202 0 0 32.918158 38.686292 203 0 0 32.844584 38.645019 204 0 0 32.94858 38.733831 205 0 0 32.849336 38.669812 206 0 0 32.886501 38.675127 207 0 0 32.856899 38.665607 208 0 0 32.803723 38.638448 209 0 0 32.777251 38.606174 210 0 0 32.819124 38.638162 211 0 0 32.817181 38.660283 212 0 0 32.754649 38.604407 213 0 0 32.726289 38.605112 214 0 0 32.758831 38.645885 215 0 0 32.709731 38.596687 216 0 0 32.602094 38.520568 217 0 0 32.624931 38.530171 218 0 0 32.64169 38.550581 219 0 0 32.562581 38.473337 220 0 0 32.678938 38.578441 221 0 0 32.668019 38.535971 222 0 0 32.592131 38.526995 223 0 0 32.50244 38.486668 224 0 0 32.440673 38.428284 225 0 0 32.515345 38.48369 226 0 0 32.522455 38.46986 227 0 0 32.320955 38.342116 228 0 0 32.345472 38.365703 229 0 0 32.36256 38.360695 230 0 0 32.315101 38.338486 231 0 0 32.414223 38.392274 232 0 0 32.271903 38.31465 233 0 0 32.162791 38.245686 234 0 0 32.293455 38.321551 235 0 0 32.207332 38.300013 236 0 0 32.121669 38.233147 237 0 0 32.185888 38.236623 238 0 0 32.080379 38.198928 239 0 0 32.104822 38.210248 240 0 0 32.067587 38.160898 241 0 0 32.094276 38.22591 242 0 0 32.172763 38.259186 243 0 0 31.916794 38.101442 244 0 0 31.937206 38.084249 245 0 0 32.13936 38.254955 246 0 0 31.91058 38.130056 247 0 0 31.980544 38.093467 248 0 0 31.763359 38.023488 249 0 0 31.774067 38.012034 250 0 0 31.818773 38.078893 251 0 0 31.504605 37.778554 252 0 0 31.572541 37.890728 253 0 0 31.863182 38.1083 254 0 0 31.724752 38.015177 255 0 0 31.505787 37.805916 256 0 0 31.601081 37.908228 257 0 0 31.41571 37.730764 258 0 0 31.571212 37.938093 259 0 0 31.239814 37.658906 260 0 0 31.171304 37.640832 261 0 0 31.157248 37.619984 262 0 0 31.055392 37.516995 263 0 0 30.961028 37.523911 264 0 0 30.821695 37.380325 265 0 0 30.910199 37.467208 266 0 0 30.747005 37.340399 267 0 0 30.744 37.324706 268 0 0 30.766586 37.404843 269 0 0 30.884692 37.455268 270 0 0 30.392533 37.170535 271 0 0 30.153056 36.900873 272 0 0 30.395373 37.154224 273 0 0 29.86244 36.83002 274 0 0 30.066152 36.947078 275 0 0 29.858268 36.619235 276 0 0 29.94172 36.817273 277 0 0 29.733056 36.508125 278 0 0 29.808563 36.687054 279 0 0 29.785214 36.680051 280 0 0 29.304405 36.292571 281 0 0 29.505078 36.46784 282 0 0 29.472753 36.412597 283 0 0 29.35277 36.465986 284 0 0 29.418712 36.488753 285 0 0 29.486726 36.433896 286 0 0 29.534454 36.49916 287 0 0 29.21231 36.319358 288 0 0 28.844193 35.99402 289 0 0 29.216216 36.278946 290 0 0 29.438166 36.454869 291 0 0 29.013544 36.173815 292 0 0 29.058403 36.16766 293 0 0 28.783851 35.95528 294 0 0 28.981675 36.15445 295 0 0 29.041494 36.142001 296 0 0 28.966276 36.322581 297 0 0 29.113178 36.183979 298 0 0 29.390805 36.340996 299 0 0 28.917832 36.065851 300 0 0 28.54479 35.902498 301 0 0 28.442495 35.79922 302 0 0 29.361746 36.537769 303 0 0 28.591703 35.898108 304 0 0 27.74478 35.266048 305 0 0 28.46402 35.918114 306 0 0 28.523437 35.960069 307 0 0 28.646575 35.840183 308 0 0 28.126437 35.604406 309 0 0 28.283537 35.632114 310 0 0 28.187713 35.533561 311 0 0 28.323308 35.744361 312 0 0 28.230453 35.589849 313 0 0 28.142222 35.61037 314 0 0 27.490476 34.94127 315 0 0 28.671875 35.763889 316 0 0 28.070588 35.445098 317 0 0 27.56 35.193333 318 0 0 27.984848 35.232323 319 0 0 28.017094 35.518519 320 0 0 26.772727 34.951515 321 0 0 26.652632 35.17193 322 0 0 27.325 35.1875 323 0 0 26.119403 33.950249 324 0 0 27.271186 35.20904 325 0 0 27.08 34.746667 326 0 0 28.976744 36.20155 327 0 0 31.307692 38.017094 328 0 0 30.766667 36.988889 329 0 0 30.607143 37.369048 330 0 0 27.961538 35.833333 331 0 0 28.375 35.875 332 0 0 26.291667 33.763889 333 0 0 28.761905 35.380952 334 0 0 26 34.070175 335 0 0 30 37.254902 336 0 0 29.533333 37.511111 337 0 0 26.846154 34.307692 338 0 0 21.583333 29.388889 339 0 0 22.545455 31.969697 340 0 0 25.222222 32.481481 341 0 0 26.285714 32.904762 342 0 0 23.166667 31.277778 343 0 0 28.833333 35.333333 344 0 0 25.333333 34.277778 345 0 0 23.75 30.416667 346 0 0 30.5 35.5 347 0 0 34.666667 40.222222 348 0 0 36 41 349 0 0 32.5 39 350 0 0 25 34 351 0 0 29.5 35.833333 352 0 0 35.5 40.333333 353 0 0 36 41 354 0 0 35 40 355 0 0 36 41 356 0 0 27 34.333333