## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5408-Z0098-CAACAGATGTATGAT/441525-L5408-Z0098-CAACAGATGTATGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5408-Z0098-CAACAGATGTATGAT/441525-L5408-Z0098-CAACAGATGTATGAT_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 03:02:07 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 1000154 1000154 136 136630872 136630872 131704132 131704132 122521346 122521346 0 0 0.963941 0.896733 0 0.963941 0.896733 0 409892616 409892616 403365475 403365475 388693189 388693189 364236697 364236697 0.984076 0.948281 0.888615 0.984076 0.948281 0.888615 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 938 0 35.994131 40.995366 1 12150 0 35.984579 40.989365 2 14314 4838 35.993767 40.994642 3 36620 1366 35.982722 40.985829 4 57717 51393 35.991569 40.99317 5 115204 18103 35.995233 40.99615 6 109956 131788 35.977281 40.980573 7 198194 165418 35.977242 40.984903 8 194074 151241 35.986361 40.988726 9 244351 115306 35.957865 40.964382 10 258244 505835 35.899742 40.940348 11 303640 65444 35.931584 40.948897 12 360743 717269 35.28788 40.39731 13 348883 213021 33.831919 39.657253 14 470911 1010047 35.895178 40.935678 15 377217 383302 35.840308 40.886315 16 387342 440200 35.808317 40.829993 17 514699 1111833 35.907118 40.922098 18 553847 736915 35.740168 40.787699 19 367696 703822 35.747276 40.820522 20 519443 985408 35.902924 40.937945 21 661385 1373465 35.823696 40.872809 22 325095 550857 35.607691 40.731345 23 1061905 1237771 35.342414 40.557424 24 579668 1185629 35.31882 40.538633 25 546760 467680 35.300227 40.522796 26 1762646 2556667 35.254622 40.489693 27 359137 869069 35.256898 40.495299 28 954887 389014 35.269248 40.503611 29 2411860 5056726 35.263618 40.500348 30 758115 43584 35.250935 40.489617 31 2284183 828235 35.240777 40.482121 32 1658886 5364676 35.239324 40.479163 33 839856 131265 35.236904 40.478567 34 2420980 2740124 35.234614 40.476028 35 2169635 3733716 35.246124 40.48504 36 112389691 2191625 35.275123 40.503801 37 0 4124516 35.265757 40.498525 38 0 400754 35.256954 40.492907 39 0 4897997 35.254118 40.489705 40 0 1 35.253828 40.489195 41 0 364236696 35.232844 40.474532 42 0 0 35.228528 40.470954 43 0 0 35.238749 40.477625 44 0 0 35.242874 40.480756 45 0 0 35.24409 40.481814 46 0 0 35.238313 40.476395 47 0 0 35.228951 40.471804 48 0 0 35.224301 40.467117 49 0 0 35.209741 40.458039 50 0 0 35.201729 40.45135 51 0 0 35.197385 40.448754 52 0 0 35.183969 40.439226 53 0 0 35.170223 40.43044 54 0 0 35.158471 40.420164 55 0 0 35.144839 40.410885 56 0 0 35.120633 40.39345 57 0 0 35.102262 40.381373 58 0 0 35.066992 40.354776 59 0 0 35.030504 40.327019 60 0 0 34.988606 40.297768 61 0 0 34.936231 40.258092 62 0 0 34.885449 40.218139 63 0 0 34.82731 40.174355 64 0 0 34.771582 40.131067 65 0 0 34.705234 40.082829 66 0 0 34.633493 40.029658 67 0 0 34.559503 39.97438 68 0 0 34.473056 39.910585 69 0 0 34.393353 39.848067 70 0 0 34.298172 39.773444 71 0 0 34.208548 39.701439 72 0 0 34.115261 39.628061 73 0 0 34.018245 39.548187 74 0 0 33.924806 39.476103 75 0 0 33.82047 39.395193 76 0 0 33.730505 39.32633 77 0 0 33.648935 39.263195 78 0 0 33.564031 39.196912 79 0 0 33.487486 39.138633 80 0 0 33.410371 39.071609 81 0 0 33.343536 39.018267 82 0 0 33.290016 38.973531 83 0 0 33.242795 38.936678 84 0 0 33.201821 38.901973 85 0 0 33.165922 38.871883 86 0 0 33.124108 38.836572 87 0 0 33.104189 38.819131 88 0 0 33.062726 38.784395 89 0 0 33.036143 38.762991 90 0 0 32.996937 38.729079 91 0 0 32.971686 38.700997 92 0 0 32.934424 38.667629 93 0 0 32.91439 38.650362 94 0 0 32.881399 38.62187 95 0 0 32.853697 38.596733 96 0 0 32.831151 38.581793 97 0 0 32.837237 38.584176 98 0 0 32.821941 38.572307 99 0 0 32.83636 38.583706 100 0 0 32.854225 38.597066 101 0 0 32.88046 38.614922 102 0 0 32.922931 38.64731 103 0 0 32.960777 38.674759 104 0 0 32.993508 38.699091 105 0 0 33.023269 38.722098 106 0 0 33.047399 38.736596 107 0 0 33.085128 38.764409 108 0 0 33.102603 38.779558 109 0 0 33.112355 38.787986 110 0 0 33.102762 38.780372 111 0 0 33.098722 38.778988 112 0 0 33.081496 38.759599 113 0 0 33.040767 38.725348 114 0 0 33.011548 38.699611 115 0 0 32.969388 38.664283 116 0 0 32.938738 38.645223 117 0 0 32.926656 38.635905 118 0 0 32.926103 38.638073 119 0 0 32.937359 38.65244 120 0 0 32.935051 38.649063 121 0 0 32.948318 38.660495 122 0 0 32.971503 38.675423 123 0 0 32.976176 38.674095 124 0 0 33.017301 38.706345 125 0 0 33.035838 38.719493 126 0 0 33.055053 38.731873 127 0 0 33.071935 38.742224 128 0 0 33.07679 38.743101 129 0 0 33.069606 38.736619 130 0 0 33.071016 38.736672 131 0 0 33.064742 38.730524 132 0 0 33.065702 38.729132 133 0 0 33.068983 38.733406 134 0 0 33.047797 38.712123 135 0 0 33.062923 38.722805 136 0 0 33.056028 38.716584 137 0 0 33.049244 38.705493 138 0 0 33.055982 38.717238 139 0 0 33.06247 38.724994 140 0 0 33.071137 38.732443 141 0 0 33.123002 38.774976 142 0 0 33.137369 38.783619 143 0 0 33.136531 38.781911 144 0 0 33.13756 38.781677 145 0 0 33.123329 38.768491 146 0 0 33.134829 38.771614 147 0 0 33.097381 38.740475 148 0 0 33.086502 38.73374 149 0 0 33.062715 38.707555 150 0 0 33.046954 38.700797 151 0 0 33.005764 38.663776 152 0 0 32.994478 38.659183 153 0 0 32.983375 38.649869 154 0 0 32.993161 38.657365 155 0 0 32.966897 38.633866 156 0 0 32.966625 38.634729 157 0 0 32.9638 38.628731 158 0 0 32.989606 38.645969 159 0 0 33.023 38.672293 160 0 0 33.031255 38.678294 161 0 0 33.052039 38.694656 162 0 0 33.092403 38.731434 163 0 0 33.096992 38.72608 164 0 0 33.099429 38.730208 165 0 0 33.108368 38.739782 166 0 0 33.068144 38.70271 167 0 0 33.057692 38.691402 168 0 0 32.994772 38.640546 169 0 0 32.938526 38.584256 170 0 0 32.883218 38.540639 171 0 0 32.82876 38.498884 172 0 0 32.806554 38.475658 173 0 0 32.797283 38.468911 174 0 0 32.780294 38.457545 175 0 0 32.779135 38.452723 176 0 0 32.769228 38.452035 177 0 0 32.809131 38.484127 178 0 0 32.817804 38.489591 179 0 0 32.858814 38.521085 180 0 0 32.869781 38.535544 181 0 0 32.870151 38.532213 182 0 0 32.94176 38.592179 183 0 0 32.97904 38.627353 184 0 0 33.010845 38.648113 185 0 0 33.050806 38.683664 186 0 0 33.104923 38.722391 187 0 0 33.109715 38.725134 188 0 0 33.125188 38.736325 189 0 0 33.172914 38.779525 190 0 0 33.135511 38.747835 191 0 0 33.136497 38.752449 192 0 0 33.140912 38.75972 193 0 0 33.103753 38.729927 194 0 0 33.072234 38.715002 195 0 0 33.061009 38.712409 196 0 0 33.076376 38.728876 197 0 0 33.063483 38.725425 198 0 0 33.021978 38.701711 199 0 0 33.008182 38.699908 200 0 0 33.012214 38.711747 201 0 0 32.988248 38.695313 202 0 0 32.987646 38.697031 203 0 0 32.919755 38.656389 204 0 0 32.919133 38.667555 205 0 0 32.878813 38.641872 206 0 0 32.848831 38.626873 207 0 0 32.846491 38.628102 208 0 0 32.790242 38.597999 209 0 0 32.790623 38.606237 210 0 0 32.778112 38.601063 211 0 0 32.703227 38.543242 212 0 0 32.695462 38.550185 213 0 0 32.651426 38.517261 214 0 0 32.629236 38.505418 215 0 0 32.594773 38.478413 216 0 0 32.586804 38.477736 217 0 0 32.596932 38.491034 218 0 0 32.515278 38.432871 219 0 0 32.483114 38.417969 220 0 0 32.511265 38.434884 221 0 0 32.490065 38.418435 222 0 0 32.444284 38.392271 223 0 0 32.416852 38.372411 224 0 0 32.431775 38.392367 225 0 0 32.412959 38.376483 226 0 0 32.381161 38.354907 227 0 0 32.291262 38.296323 228 0 0 32.31623 38.314357 229 0 0 32.32663 38.323758 230 0 0 32.372761 38.356345 231 0 0 32.322751 38.314188 232 0 0 32.369086 38.351429 233 0 0 32.274673 38.304909 234 0 0 32.289517 38.308795 235 0 0 32.255476 38.279298 236 0 0 32.203917 38.253773 237 0 0 32.212918 38.268141 238 0 0 32.171842 38.233817 239 0 0 32.099457 38.192095 240 0 0 32.190762 38.259385 241 0 0 32.104185 38.216152 242 0 0 31.996558 38.111782 243 0 0 31.950695 38.09018 244 0 0 31.964118 38.09112 245 0 0 32.050045 38.150047 246 0 0 31.988235 38.113081 247 0 0 31.969244 38.114976 248 0 0 31.988419 38.106302 249 0 0 31.874907 38.066708 250 0 0 31.869582 38.068308 251 0 0 31.757221 37.968677 252 0 0 31.850974 38.03053 253 0 0 31.712701 37.961002 254 0 0 31.705212 37.954545 255 0 0 31.732255 37.966018 256 0 0 31.678336 37.911222 257 0 0 31.608853 37.884455 258 0 0 31.637108 37.917775 259 0 0 31.573431 37.88217 260 0 0 31.466806 37.813284 261 0 0 31.434876 37.799319 262 0 0 31.493469 37.828124 263 0 0 31.510031 37.827761 264 0 0 31.432199 37.800247 265 0 0 31.344522 37.737527 266 0 0 31.270656 37.678875 267 0 0 31.212356 37.66861 268 0 0 31.246482 37.685121 269 0 0 31.063278 37.559031 270 0 0 31.121356 37.586289 271 0 0 30.982664 37.502079 272 0 0 30.84337 37.419639 273 0 0 30.836764 37.408855 274 0 0 30.783613 37.377255 275 0 0 30.796393 37.354488 276 0 0 30.662863 37.318916 277 0 0 30.544799 37.181263 278 0 0 30.432867 37.122574 279 0 0 30.48853 37.184777 280 0 0 30.321373 37.072379 281 0 0 30.387158 37.103041 282 0 0 30.2956 37.04166 283 0 0 30.086461 36.92672 284 0 0 29.888029 36.795838 285 0 0 30.028531 36.8818 286 0 0 29.913528 36.816636 287 0 0 29.991901 36.827023 288 0 0 29.60809 36.611315 289 0 0 29.464671 36.490752 290 0 0 29.511322 36.573967 291 0 0 29.432744 36.433454 292 0 0 29.486671 36.487185 293 0 0 29.249147 36.298369 294 0 0 29.589573 36.536177 295 0 0 29.513574 36.519497 296 0 0 29.332132 36.335651 297 0 0 29.249062 36.303217 298 0 0 29.034656 36.193404 299 0 0 29.154748 36.216491 300 0 0 28.755089 35.932963 301 0 0 28.950016 36.131785 302 0 0 29.053602 36.191988 303 0 0 28.741831 35.983244 304 0 0 28.911608 36.090035 305 0 0 28.719038 35.995324 306 0 0 28.77825 35.956386 307 0 0 28.32404 35.696527 308 0 0 28.596483 35.889432 309 0 0 28.68897 35.885346 310 0 0 28.682399 35.839349 311 0 0 28.936861 36.123472 312 0 0 28.838226 36.021309 313 0 0 28.33428 35.628815 314 0 0 28.361196 35.586401 315 0 0 28.353135 35.687294 316 0 0 28.288305 35.664551 317 0 0 28.298918 35.575549 318 0 0 28.029508 35.467031 319 0 0 27.998795 35.238956 320 0 0 28.114667 35.508 321 0 0 28.862832 35.921829 322 0 0 28.136134 35.476751 323 0 0 27.619403 34.97699 324 0 0 27.914851 35.251485 325 0 0 27.871179 35.534934 326 0 0 27.534146 35.026829 327 0 0 28.201117 35.506518 328 0 0 27.605678 35.288118 329 0 0 26.612245 34.114512 330 0 0 29.281853 36.395109 331 0 0 27.515419 34.976505 332 0 0 28.348259 35.555556 333 0 0 28.017442 35.722868 334 0 0 27.653333 35.353333 335 0 0 27.92 35.570667 336 0 0 28.590909 35.981818 337 0 0 27.89899 35.080808 338 0 0 29.476744 36.627907 339 0 0 28.74359 35.397436 340 0 0 26.850746 34.61194 341 0 0 27.566667 35.127778 342 0 0 27.672727 35.054545 343 0 0 28.428571 35.979592 344 0 0 24.578947 33.22807 345 0 0 27.03125 34.65625 346 0 0 28.6 36.533333 347 0 0 25.565217 33.956522 348 0 0 28.333333 36.746032 349 0 0 27.823529 36.078431 350 0 0 25.642857 33.214286 351 0 0 30.071429 36.238095 352 0 0 30.5 36.888889 353 0 0 27.142857 36.142857 354 0 0 26.333333 34.333333 355 0 0 23.5 32.111111 356 0 0 25 31.722222 357 0 0 33.75 39.5 358 0 0 22.75 31.166667 359 0 0 31.75 38.916667 360 0 0 29 34.666667 361 0 0 31 38.5 362 0 0 13.5 24.5 363 0 0 28 36.333333 364 0 0 36 41 365 0 0 36 41 366 0 0 9 16.666667 367 0 0 31 38 368 0 0 26 33 369 0 0 11 23 370 0 0 36 41 371 0 0 36 41 372 0 0 36 41 373 0 0 36 40.333333 374 0 0 10 25 375 0 0 7 25.666667 376 0 0 29 37 377 0 0 17 26 378 0 0 31 37.333333 379 0 0 6 11.666667 380 0 0 34 39 381 0 0 6 12.666667 382 0 0 36 41