## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5398-Z0086-CAACTATCTGCAGAT/441525-L5398-Z0086-CAACTATCTGCAGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5398-Z0086-CAACTATCTGCAGAT/441525-L5398-Z0086-CAACTATCTGCAGAT_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 02:54:28 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 1000302 1000302 127 127448284 127448284 122660670 122660670 113564197 113564197 0 0 0.962435 0.891061 0 0.962435 0.891061 0 382344852 382344852 376003207 376003207 361492953 361492953 337425233 337425233 0.983414 0.945463 0.882515 0.983414 0.945463 0.882515 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 818 0 35.994627 40.995809 1 10499 0 35.985646 40.990344 2 12835 4075 35.994093 40.995044 3 33215 1189 35.977601 40.98165 4 53703 45358 35.990243 40.99219 5 106558 16834 35.994478 40.995689 6 111298 118626 35.974639 40.978293 7 187722 151376 35.97534 40.983569 8 190501 145248 35.987341 40.989705 9 232963 105126 35.958533 40.965163 10 242049 498509 35.89408 40.934799 11 289884 58624 35.928362 40.946658 12 342667 689561 35.192611 40.324804 13 346535 207815 33.579427 39.512234 14 451703 974359 35.870054 40.919835 15 361675 364539 35.836737 40.882165 16 384650 445376 35.781124 40.805472 17 514282 1103282 35.896964 40.91245 18 543069 710915 35.743524 40.788747 19 370988 700833 35.753797 40.816169 20 493766 1006450 35.908938 40.939869 21 644409 1331588 35.85055 40.891792 22 318754 559591 35.626252 40.741985 23 1025181 1180636 35.333138 40.540417 24 568331 1151842 35.344052 40.552603 25 540658 469295 35.335282 40.547469 26 1753067 2526860 35.275043 40.50177 27 351620 856121 35.287451 40.514241 28 949888 364598 35.298266 40.522928 29 2450799 5063273 35.298305 40.520987 30 739019 39926 35.288 40.514719 31 2279240 778834 35.286876 40.512228 32 1550628 5400727 35.275577 40.503317 33 808646 118197 35.275199 40.503258 34 2377905 2509879 35.266526 40.497014 35 2148002 3805080 35.277584 40.505425 36 103660757 1999689 35.302862 40.52368 37 0 4184119 35.301059 40.523702 38 0 357052 35.290923 40.516495 39 0 4874217 35.296731 40.519201 40 0 0 35.287981 40.513634 41 0 337425233 35.271366 40.50051 42 0 0 35.26139 40.494617 43 0 0 35.266064 40.496732 44 0 0 35.272829 40.500666 45 0 0 35.274077 40.501814 46 0 0 35.26456 40.497065 47 0 0 35.259499 40.492453 48 0 0 35.248016 40.485079 49 0 0 35.24138 40.478804 50 0 0 35.240938 40.479299 51 0 0 35.226774 40.470249 52 0 0 35.204419 40.453728 53 0 0 35.183078 40.438058 54 0 0 35.174437 40.430527 55 0 0 35.140595 40.403352 56 0 0 35.110723 40.383978 57 0 0 35.093468 40.372321 58 0 0 35.050459 40.337964 59 0 0 34.993759 40.299733 60 0 0 34.936624 40.261431 61 0 0 34.874112 40.213632 62 0 0 34.805955 40.158614 63 0 0 34.727819 40.097781 64 0 0 34.638439 40.02748 65 0 0 34.537669 39.95491 66 0 0 34.434182 39.875065 67 0 0 34.327575 39.795592 68 0 0 34.208282 39.702297 69 0 0 34.072707 39.599509 70 0 0 33.938568 39.494398 71 0 0 33.810232 39.389078 72 0 0 33.662225 39.271717 73 0 0 33.54107 39.175436 74 0 0 33.416861 39.076197 75 0 0 33.317703 38.999998 76 0 0 33.216678 38.920432 77 0 0 33.139657 38.862294 78 0 0 33.058422 38.800693 79 0 0 32.999173 38.750205 80 0 0 32.947912 38.708334 81 0 0 32.908223 38.67227 82 0 0 32.878283 38.644966 83 0 0 32.862322 38.632176 84 0 0 32.847631 38.615627 85 0 0 32.828152 38.598769 86 0 0 32.799397 38.572089 87 0 0 32.759674 38.539888 88 0 0 32.732003 38.513937 89 0 0 32.697963 38.483359 90 0 0 32.651621 38.442361 91 0 0 32.610943 38.405617 92 0 0 32.574485 38.372716 93 0 0 32.534049 38.340776 94 0 0 32.505024 38.315595 95 0 0 32.476615 38.292625 96 0 0 32.46429 38.283707 97 0 0 32.457096 38.275347 98 0 0 32.45995 38.275548 99 0 0 32.493693 38.30508 100 0 0 32.522473 38.326945 101 0 0 32.576796 38.369756 102 0 0 32.618384 38.400288 103 0 0 32.673817 38.443858 104 0 0 32.728248 38.482312 105 0 0 32.760249 38.503774 106 0 0 32.781159 38.518229 107 0 0 32.794628 38.525335 108 0 0 32.804055 38.534481 109 0 0 32.796143 38.526738 110 0 0 32.773788 38.507583 111 0 0 32.758351 38.49624 112 0 0 32.712138 38.457308 113 0 0 32.650499 38.409115 114 0 0 32.620782 38.383346 115 0 0 32.575122 38.346149 116 0 0 32.545731 38.32523 117 0 0 32.523562 38.309292 118 0 0 32.524003 38.314411 119 0 0 32.541795 38.326982 120 0 0 32.52773 38.316571 121 0 0 32.554281 38.339773 122 0 0 32.564309 38.346376 123 0 0 32.58627 38.358728 124 0 0 32.618142 38.383581 125 0 0 32.643733 38.402244 126 0 0 32.648283 38.396352 127 0 0 32.663935 38.407504 128 0 0 32.657329 38.397756 129 0 0 32.631827 38.379314 130 0 0 32.616924 38.365432 131 0 0 32.60977 38.357878 132 0 0 32.578474 38.333685 133 0 0 32.597373 38.344655 134 0 0 32.596391 38.340001 135 0 0 32.580637 38.327354 136 0 0 32.584686 38.332945 137 0 0 32.561366 38.310949 138 0 0 32.575012 38.325795 139 0 0 32.581996 38.330336 140 0 0 32.596459 38.347577 141 0 0 32.637419 38.371968 142 0 0 32.650886 38.383581 143 0 0 32.650855 38.383521 144 0 0 32.638561 38.368156 145 0 0 32.648361 38.379307 146 0 0 32.618997 38.351361 147 0 0 32.570031 38.302766 148 0 0 32.561192 38.299644 149 0 0 32.523717 38.270093 150 0 0 32.503828 38.24979 151 0 0 32.472193 38.230225 152 0 0 32.447683 38.208825 153 0 0 32.448662 38.208376 154 0 0 32.437484 38.19916 155 0 0 32.46723 38.221319 156 0 0 32.48957 38.235756 157 0 0 32.475264 38.226459 158 0 0 32.516045 38.263257 159 0 0 32.541469 38.278619 160 0 0 32.590732 38.316557 161 0 0 32.624765 38.342987 162 0 0 32.682718 38.385113 163 0 0 32.696191 38.398313 164 0 0 32.679574 38.388627 165 0 0 32.705958 38.411763 166 0 0 32.718604 38.415629 167 0 0 32.704399 38.398997 168 0 0 32.655407 38.35694 169 0 0 32.648463 38.349827 170 0 0 32.604209 38.311005 171 0 0 32.588599 38.297653 172 0 0 32.590643 38.29991 173 0 0 32.634786 38.338911 174 0 0 32.632543 38.347939 175 0 0 32.665837 38.364706 176 0 0 32.689367 38.389552 177 0 0 32.717205 38.408945 178 0 0 32.778248 38.464784 179 0 0 32.79748 38.478682 180 0 0 32.871329 38.53576 181 0 0 32.92526 38.585948 182 0 0 32.951905 38.607902 183 0 0 33.000109 38.647394 184 0 0 33.011573 38.661626 185 0 0 33.032154 38.675708 186 0 0 33.028488 38.679605 187 0 0 33.061164 38.710201 188 0 0 33.078849 38.714982 189 0 0 33.092042 38.729945 190 0 0 33.067259 38.715201 191 0 0 33.090726 38.728262 192 0 0 33.052369 38.713034 193 0 0 33.06299 38.725934 194 0 0 33.072392 38.735141 195 0 0 33.00824 38.700816 196 0 0 33.01571 38.707952 197 0 0 32.991194 38.694612 198 0 0 33.020684 38.716824 199 0 0 32.951438 38.680151 200 0 0 33.001541 38.716601 201 0 0 32.966133 38.703541 202 0 0 32.949869 38.699354 203 0 0 32.94536 38.695846 204 0 0 32.93181 38.699964 205 0 0 32.908902 38.674076 206 0 0 32.917455 38.696733 207 0 0 32.884888 38.670885 208 0 0 32.877791 38.669168 209 0 0 32.813902 38.627081 210 0 0 32.831422 38.647734 211 0 0 32.814024 38.637627 212 0 0 32.858382 38.667022 213 0 0 32.82643 38.648257 214 0 0 32.77339 38.606858 215 0 0 32.764733 38.595531 216 0 0 32.747192 38.598993 217 0 0 32.768081 38.630712 218 0 0 32.693814 38.573399 219 0 0 32.614859 38.528273 220 0 0 32.616682 38.522494 221 0 0 32.59702 38.504488 222 0 0 32.656695 38.549338 223 0 0 32.60879 38.518516 224 0 0 32.58179 38.50366 225 0 0 32.528036 38.459434 226 0 0 32.490937 38.432168 227 0 0 32.597771 38.509227 228 0 0 32.58767 38.506445 229 0 0 32.452843 38.431531 230 0 0 32.491831 38.457246 231 0 0 32.467403 38.44127 232 0 0 32.464307 38.440404 233 0 0 32.35787 38.370221 234 0 0 32.414497 38.41341 235 0 0 32.27297 38.315895 236 0 0 32.309551 38.343817 237 0 0 32.326326 38.361509 238 0 0 32.291279 38.334839 239 0 0 32.252335 38.321875 240 0 0 32.217994 38.282939 241 0 0 32.148215 38.227379 242 0 0 32.165174 38.251779 243 0 0 32.108372 38.237439 244 0 0 32.016641 38.147172 245 0 0 32.07164 38.192356 246 0 0 31.894478 38.051039 247 0 0 31.929052 38.094044 248 0 0 32.009083 38.146643 249 0 0 31.950505 38.133562 250 0 0 31.953811 38.119442 251 0 0 31.812765 38.039529 252 0 0 31.931112 38.110242 253 0 0 31.843382 38.069145 254 0 0 31.880587 38.117698 255 0 0 31.71985 37.970429 256 0 0 31.592751 37.908058 257 0 0 31.591404 37.906279 258 0 0 31.726677 38.001747 259 0 0 31.518641 37.856471 260 0 0 31.56005 37.880402 261 0 0 31.526397 37.862263 262 0 0 31.541304 37.886206 263 0 0 31.34359 37.756365 264 0 0 31.382516 37.769742 265 0 0 31.496743 37.833569 266 0 0 31.37984 37.76877 267 0 0 31.218903 37.648833 268 0 0 31.149537 37.584636 269 0 0 31.177174 37.601346 270 0 0 31.115482 37.565408 271 0 0 30.846803 37.429622 272 0 0 30.835823 37.422034 273 0 0 30.876018 37.413275 274 0 0 30.69072 37.282798 275 0 0 30.847915 37.441467 276 0 0 30.679622 37.320862 277 0 0 30.599592 37.299115 278 0 0 30.33308 37.063471 279 0 0 30.425462 37.133139 280 0 0 30.290895 37.023444 281 0 0 30.142246 36.945044 282 0 0 30.204545 36.948221 283 0 0 30.203303 36.983344 284 0 0 30.04318 36.845586 285 0 0 30.083676 36.896662 286 0 0 29.600985 36.578388 287 0 0 29.77929 36.689921 288 0 0 29.716084 36.720027 289 0 0 29.773046 36.690816 290 0 0 29.508579 36.492761 291 0 0 29.600724 36.576762 292 0 0 29.509832 36.509639 293 0 0 29.51426 36.48544 294 0 0 29.463445 36.464168 295 0 0 29.698223 36.685191 296 0 0 29.383137 36.380776 297 0 0 29.266737 36.344726 298 0 0 29.272056 36.309216 299 0 0 29.042643 36.15687 300 0 0 29.13753 36.231756 301 0 0 28.798658 36.011885 302 0 0 29.007512 36.168508 303 0 0 29.019462 36.156472 304 0 0 28.855334 36.116902 305 0 0 29.0154 36.147844 306 0 0 28.896139 36.119086 307 0 0 28.610367 35.840613 308 0 0 28.587943 35.877564 309 0 0 28.3996 35.705137 310 0 0 28.142653 35.549691 311 0 0 28.548714 35.759158 312 0 0 27.843154 35.218257 313 0 0 28.287757 35.624069 314 0 0 28.608612 35.881978 315 0 0 28.22314 35.657369 316 0 0 28.125416 35.440622 317 0 0 28.191847 35.609512 318 0 0 28.472222 35.660494 319 0 0 28.324047 35.740958 320 0 0 28.225806 35.655914 321 0 0 28.068541 35.446397 322 0 0 28.511628 35.827519 323 0 0 28.109474 35.471579 324 0 0 28.7 35.92619 325 0 0 29.162667 36.072889 326 0 0 29.023256 36.110465 327 0 0 28.329073 35.684771 328 0 0 27.805755 35.184652 329 0 0 27.378486 34.85923 330 0 0 27.03125 34.822917 331 0 0 27.914141 35.244108 332 0 0 28.837079 36.054307 333 0 0 28.923077 36.017094 334 0 0 29.751773 36.546099 335 0 0 28.330645 35.454301 336 0 0 27.841121 35.676012 337 0 0 26.722222 34.481481 338 0 0 25.378378 33.536036 339 0 0 27.9375 35.354167 340 0 0 26.842105 34.789474 341 0 0 28.955556 36.044444 342 0 0 26.674419 34.271318 343 0 0 30.513514 37.405405 344 0 0 26.5 34.384615 345 0 0 24.16 32.466667 346 0 0 24 31.80303 347 0 0 29.4 36.433333 348 0 0 25.5 33.425926 349 0 0 24.357143 32.071429 350 0 0 25.166667 34.388889 351 0 0 27.818182 35.151515 352 0 0 27.857143 35.761905 353 0 0 27 36.75 354 0 0 22.5 32.666667 355 0 0 32 37.333333 356 0 0 18.5 25.333333 357 0 0 35 39.666667 358 0 0 23 31 359 0 0 29 35.666667 360 0 0 34 39 361 0 0 32 37 362 0 0 32 37 363 0 0 6 12.666667 364 0 0 36 41