## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5395-Z0081-CTTGATCATACAGAT/441525-L5395-Z0081-CTTGATCATACAGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5395-Z0081-CTTGATCATACAGAT/441525-L5395-Z0081-CTTGATCATACAGAT_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 03:00:01 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 999408 999408 137 137350955 137350955 132511086 132511086 123434490 123434490 0 0 0.964763 0.89868 0 0.964763 0.89868 0 412052865 412052865 405632957 405632957 391132777 391132777 366717279 366717279 0.98442 0.94923 0.889976 0.98442 0.94923 0.889976 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 855 0 35.990662 40.992577 1 11213 0 35.982788 40.987578 2 13645 4487 35.995463 40.996254 3 34344 1272 35.985598 40.988271 4 55935 47977 35.992379 40.993833 5 110341 17530 35.996042 40.996528 6 109536 124503 35.979455 40.983737 7 193878 158799 35.983971 40.988869 8 193575 147822 35.991458 40.993002 9 242686 110386 35.961319 40.967317 10 251301 504347 35.873065 40.925896 11 297609 61836 35.908798 40.931823 12 349315 705284 35.268632 40.389155 13 347100 211380 33.886482 39.691388 14 455304 991644 35.879434 40.926223 15 368543 375324 35.832493 40.880877 16 380946 436395 35.786242 40.80938 17 510029 1102769 35.890853 40.907969 18 547962 722687 35.74273 40.789997 19 365752 695466 35.739076 40.809043 20 507673 982510 35.894952 40.931653 21 655612 1365755 35.809014 40.857311 22 319587 545023 35.576214 40.708375 23 1036097 1209655 35.238891 40.450113 24 575987 1180139 35.296964 40.513052 25 533803 464654 35.316032 40.532265 26 1739578 2497124 35.231837 40.458471 27 358077 866398 35.271181 40.50318 28 941464 381792 35.258289 40.496192 29 2408718 5007130 35.24793 40.48454 30 764541 42012 35.29001 40.514515 31 2298502 808676 35.27967 40.505815 32 1620383 5343934 35.255596 40.48114 33 851442 130509 35.280075 40.505134 34 2431945 2685165 35.278925 40.505687 35 2196153 3772241 35.296707 40.519111 36 113271524 2124627 35.31452 40.531101 37 0 4178268 35.316396 40.533323 38 0 387628 35.310349 40.530233 39 0 4942438 35.306099 40.526358 40 0 0 35.29797 40.518536 41 0 366717279 35.286465 40.510526 42 0 0 35.278066 40.503699 43 0 0 35.27992 40.505131 44 0 0 35.294493 40.516338 45 0 0 35.295698 40.516548 46 0 0 35.278961 40.504356 47 0 0 35.273264 40.499346 48 0 0 35.253692 40.486457 49 0 0 35.247231 40.482177 50 0 0 35.250136 40.48672 51 0 0 35.246584 40.483245 52 0 0 35.202355 40.451993 53 0 0 35.175205 40.443199 54 0 0 35.186199 40.447737 55 0 0 35.177477 40.440555 56 0 0 35.125983 40.416344 57 0 0 35.1715 40.431961 58 0 0 35.158802 40.420445 59 0 0 35.136485 40.404054 60 0 0 35.104207 40.380763 61 0 0 35.068893 40.354268 62 0 0 35.030815 40.324271 63 0 0 34.982475 40.289045 64 0 0 34.945253 40.259446 65 0 0 34.888649 40.220598 66 0 0 34.832859 40.176915 67 0 0 34.775747 40.134704 68 0 0 34.710409 40.087622 69 0 0 34.636709 40.030786 70 0 0 34.559982 39.971919 71 0 0 34.471169 39.904524 72 0 0 34.391678 39.839014 73 0 0 34.304985 39.768249 74 0 0 34.21598 39.699997 75 0 0 34.128289 39.629562 76 0 0 34.032402 39.555677 77 0 0 33.949565 39.494828 78 0 0 33.85218 39.419789 79 0 0 33.76425 39.349914 80 0 0 33.706435 39.304202 81 0 0 33.625521 39.237879 82 0 0 33.559292 39.18564 83 0 0 33.501366 39.135968 84 0 0 33.451328 39.096884 85 0 0 33.402815 39.060419 86 0 0 33.357458 39.019351 87 0 0 33.32555 38.993383 88 0 0 33.272216 38.949562 89 0 0 33.22393 38.909442 90 0 0 33.181777 38.871035 91 0 0 33.14038 38.831766 92 0 0 33.095761 38.79636 93 0 0 33.067961 38.772444 94 0 0 33.017182 38.728949 95 0 0 32.988798 38.70544 96 0 0 32.970511 38.688665 97 0 0 32.94935 38.672584 98 0 0 32.931384 38.656644 99 0 0 32.931537 38.654598 100 0 0 32.945389 38.667999 101 0 0 32.970468 38.687623 102 0 0 33.007504 38.714418 103 0 0 33.039009 38.734668 104 0 0 33.07122 38.760271 105 0 0 33.076021 38.757065 106 0 0 33.108135 38.778827 107 0 0 33.113071 38.785591 108 0 0 33.117303 38.787701 109 0 0 33.130071 38.799173 110 0 0 33.116996 38.787397 111 0 0 33.088007 38.766181 112 0 0 33.06664 38.743851 113 0 0 33.01358 38.698453 114 0 0 32.964309 38.659949 115 0 0 32.909826 38.615301 116 0 0 32.876547 38.59208 117 0 0 32.866086 38.585411 118 0 0 32.866568 38.590051 119 0 0 32.852914 38.581818 120 0 0 32.843999 38.57352 121 0 0 32.854533 38.580506 122 0 0 32.8614 38.583603 123 0 0 32.869708 38.589139 124 0 0 32.896861 38.605987 125 0 0 32.904303 38.611517 126 0 0 32.939007 38.632794 127 0 0 32.946851 38.639224 128 0 0 32.943921 38.633534 129 0 0 32.939699 38.625732 130 0 0 32.923931 38.610704 131 0 0 32.919826 38.609635 132 0 0 32.882426 38.577697 133 0 0 32.890094 38.58229 134 0 0 32.905083 38.594528 135 0 0 32.887061 38.577534 136 0 0 32.882273 38.57142 137 0 0 32.876315 38.568182 138 0 0 32.863296 38.557713 139 0 0 32.878637 38.573556 140 0 0 32.888984 38.582014 141 0 0 32.941426 38.622743 142 0 0 32.944424 38.624449 143 0 0 32.945428 38.620734 144 0 0 32.950554 38.623371 145 0 0 32.930544 38.607564 146 0 0 32.917658 38.596007 147 0 0 32.902166 38.58281 148 0 0 32.86551 38.549651 149 0 0 32.840787 38.526864 150 0 0 32.803747 38.498019 151 0 0 32.77757 38.476166 152 0 0 32.785972 38.483815 153 0 0 32.751188 38.458984 154 0 0 32.758061 38.461717 155 0 0 32.754755 38.457986 156 0 0 32.760327 38.461767 157 0 0 32.756519 38.454184 158 0 0 32.793395 38.484468 159 0 0 32.804834 38.491984 160 0 0 32.805634 38.496861 161 0 0 32.842917 38.523994 162 0 0 32.876655 38.548266 163 0 0 32.901898 38.56983 164 0 0 32.877188 38.545703 165 0 0 32.891358 38.560506 166 0 0 32.871117 38.54098 167 0 0 32.842564 38.519065 168 0 0 32.797761 38.474684 169 0 0 32.7643 38.445548 170 0 0 32.688355 38.380607 171 0 0 32.635397 38.336448 172 0 0 32.645739 38.345259 173 0 0 32.619723 38.328302 174 0 0 32.612754 38.317525 175 0 0 32.617681 38.321837 176 0 0 32.637377 38.344751 177 0 0 32.659804 38.357744 178 0 0 32.695015 38.38759 179 0 0 32.7179 38.404813 180 0 0 32.786234 38.458926 181 0 0 32.809982 38.483268 182 0 0 32.846387 38.510974 183 0 0 32.917422 38.570918 184 0 0 32.936538 38.585996 185 0 0 32.958161 38.60783 186 0 0 33.006981 38.650166 187 0 0 33.026973 38.668878 188 0 0 33.058067 38.689973 189 0 0 33.093247 38.721433 190 0 0 33.068066 38.698638 191 0 0 33.057202 38.692699 192 0 0 33.050025 38.691032 193 0 0 33.051103 38.692597 194 0 0 33.025023 38.682595 195 0 0 32.971728 38.645497 196 0 0 32.957951 38.645116 197 0 0 32.973055 38.659282 198 0 0 32.959141 38.655976 199 0 0 32.933642 38.653055 200 0 0 32.904797 38.632872 201 0 0 32.909793 38.643273 202 0 0 32.894517 38.640011 203 0 0 32.827464 38.594711 204 0 0 32.786297 38.57504 205 0 0 32.786672 38.584848 206 0 0 32.77021 38.574332 207 0 0 32.717069 38.536929 208 0 0 32.715274 38.539397 209 0 0 32.648463 38.496403 210 0 0 32.693097 38.545265 211 0 0 32.670025 38.522872 212 0 0 32.558396 38.450734 213 0 0 32.605446 38.483412 214 0 0 32.56025 38.448231 215 0 0 32.574715 38.464191 216 0 0 32.498034 38.409626 217 0 0 32.50073 38.421857 218 0 0 32.5014 38.431611 219 0 0 32.486657 38.419034 220 0 0 32.418947 38.372303 221 0 0 32.446756 38.383113 222 0 0 32.443583 38.397696 223 0 0 32.362484 38.337532 224 0 0 32.329233 38.31402 225 0 0 32.325041 38.314287 226 0 0 32.314366 38.308795 227 0 0 32.30182 38.299559 228 0 0 32.283304 38.29223 229 0 0 32.271811 38.268409 230 0 0 32.242869 38.268081 231 0 0 32.228197 38.256295 232 0 0 32.114936 38.184939 233 0 0 32.189207 38.237765 234 0 0 32.14659 38.219145 235 0 0 32.099484 38.202681 236 0 0 32.052665 38.141368 237 0 0 32.097039 38.186674 238 0 0 32.072517 38.153151 239 0 0 31.998675 38.133357 240 0 0 31.989559 38.101458 241 0 0 31.996665 38.119214 242 0 0 31.959091 38.093226 243 0 0 31.90775 38.077542 244 0 0 31.832183 37.995272 245 0 0 31.867573 38.035956 246 0 0 31.806534 37.961151 247 0 0 31.842839 38.045013 248 0 0 31.794502 37.966883 249 0 0 31.772449 37.970586 250 0 0 31.649931 37.922646 251 0 0 31.693967 37.930995 252 0 0 31.631707 37.895121 253 0 0 31.551967 37.836092 254 0 0 31.676388 37.902697 255 0 0 31.597908 37.894157 256 0 0 31.539951 37.880011 257 0 0 31.454727 37.778792 258 0 0 31.454407 37.780793 259 0 0 31.341139 37.694175 260 0 0 31.390522 37.754946 261 0 0 31.324649 37.732221 262 0 0 31.29095 37.703727 263 0 0 31.341582 37.734864 264 0 0 31.065132 37.522763 265 0 0 31.144158 37.570516 266 0 0 30.925279 37.441201 267 0 0 31.012107 37.50197 268 0 0 30.956801 37.488889 269 0 0 30.990597 37.494733 270 0 0 30.745391 37.329625 271 0 0 30.787443 37.385873 272 0 0 30.815095 37.393175 273 0 0 30.520415 37.170185 274 0 0 30.683762 37.329607 275 0 0 30.633406 37.280824 276 0 0 30.513138 37.217217 277 0 0 30.310845 37.036278 278 0 0 30.527078 37.245189 279 0 0 30.16853 36.999458 280 0 0 30.186885 36.966129 281 0 0 30.267054 37.025895 282 0 0 30.033186 36.833776 283 0 0 29.963748 36.812358 284 0 0 29.823155 36.66258 285 0 0 29.912693 36.766854 286 0 0 29.880243 36.752484 287 0 0 29.878502 36.758925 288 0 0 29.861564 36.747919 289 0 0 29.545813 36.515177 290 0 0 29.672749 36.606337 291 0 0 29.421569 36.442606 292 0 0 29.429163 36.468004 293 0 0 29.428336 36.439674 294 0 0 29.031304 36.143536 295 0 0 29.192364 36.290061 296 0 0 29.212798 36.325508 297 0 0 29.1612 36.261333 298 0 0 29.298576 36.377722 299 0 0 28.805519 36.031829 300 0 0 29.014781 36.180293 301 0 0 28.673998 35.921962 302 0 0 28.798057 35.99199 303 0 0 28.604324 35.898919 304 0 0 28.907577 36.128588 305 0 0 28.92392 36.113613 306 0 0 28.394466 35.806306 307 0 0 28.68 35.95977 308 0 0 28.951183 36.117604 309 0 0 28.245656 35.609005 310 0 0 28.302698 35.756043 311 0 0 28.648995 35.923218 312 0 0 28.480431 35.800718 313 0 0 28.011702 35.601773 314 0 0 28.304147 35.640937 315 0 0 28.037759 35.556638 316 0 0 28.362319 35.685551 317 0 0 28.688385 35.988669 318 0 0 28.510972 35.842738 319 0 0 27.500858 34.93482 320 0 0 27.768224 35.204361 321 0 0 27.762605 35.27521 322 0 0 28.363636 35.623485 323 0 0 28.33 35.548333 324 0 0 28.448864 35.534091 325 0 0 27.235669 34.876858 326 0 0 28.810714 35.820238 327 0 0 28.384615 35.614035 328 0 0 28.166667 35.365497 329 0 0 28.777228 36.09901 330 0 0 28.092391 35.262681 331 0 0 28.207317 35.495935 332 0 0 27.231293 35.043084 333 0 0 27.88806 35.288557 334 0 0 28.45082 35.666667 335 0 0 28.441441 35.738739 336 0 0 27.438776 34.857143 337 0 0 29.344444 36.333333 338 0 0 28.0625 35.691667 339 0 0 29.030769 36.230769 340 0 0 27.283019 33.981132 341 0 0 27.840909 35.772727 342 0 0 26.589744 34.410256 343 0 0 26.567568 34.864865 344 0 0 25.828571 33.47619 345 0 0 28.103448 36.08046 346 0 0 27.555556 35.061728 347 0 0 24.48 33.333333 348 0 0 29.409091 35.818182 349 0 0 25.888889 33.814815 350 0 0 25.0625 34.041667 351 0 0 27.230769 36.153846 352 0 0 30.363636 37.636364 353 0 0 27.428571 36.142857 354 0 0 28.428571 37.047619 355 0 0 30 37.571429 356 0 0 27.714286 36.952381 357 0 0 30.166667 37.277778 358 0 0 33.8 39.6 359 0 0 25.4 33.2 360 0 0 36 41 361 0 0 29.75 37.666667 362 0 0 35 40.416667 363 0 0 26.25 35.25 364 0 0 34 39.666667 365 0 0 22.666667 31.888889 366 0 0 22.333333 30.333333 367 0 0 27.666667 35.666667 368 0 0 26 33.666667 369 0 0 15.666667 29.444444 370 0 0 28 35.666667 371 0 0 14.666667 23 372 0 0 29.5 38