## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5290-Z0035-CTGAATGATCTCGAT/441525-L5290-Z0035-CTGAATGATCTCGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5290-Z0035-CTGAATGATCTCGAT/441525-L5290-Z0035-CTGAATGATCTCGAT_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 1001539 1001539 142 142919316 142919316 138136284 138136284 128801194 128801194 0 0 0.966533 0.901216 0 0.966533 0.901216 0 428757948 428757948 422461811 422461811 407614837 407614837 382463549 382463549 0.985315 0.950688 0.892027 0.985315 0.950688 0.892027 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 785 0 35.994559 40.995898 1 10345 0 35.988293 40.991807 2 12972 4317 35.995513 40.996234 3 32385 1201 35.984075 40.987224 4 52382 44367 35.988953 40.991064 5 104380 15327 35.993519 40.994827 6 107609 116139 35.976055 40.981103 7 185496 149011 35.981656 40.987222 8 188172 143804 35.988345 40.990543 9 232807 100258 35.950265 40.957955 10 240236 494647 35.879988 40.925412 11 286152 56578 35.928412 40.947411 12 339605 687428 35.309767 40.419313 13 346480 199686 33.891057 39.697854 14 446705 966628 35.87704 40.926448 15 363875 362577 35.799712 40.856253 16 379735 430298 35.73821 40.767107 17 520156 1106659 35.897348 40.913405 18 549725 710787 35.716386 40.769707 19 383030 706425 35.790749 40.842842 20 513585 1016327 35.928926 40.951498 21 662180 1368693 35.842207 40.886136 22 333039 568199 35.62723 40.747865 23 1053431 1235815 35.360268 40.566657 24 587627 1198659 35.411494 40.602258 25 550941 495922 35.405052 40.597001 26 1801964 2534849 35.347624 40.551883 27 362459 897324 35.372061 40.574991 28 972528 388261 35.38896 40.585218 29 2497336 5142925 35.377337 40.576134 30 782497 41625 35.373693 40.574042 31 2386961 849286 35.369144 40.569544 32 1634482 5468346 35.361358 40.562187 33 866472 122313 35.372157 40.570115 34 2512727 2684854 35.364904 40.567968 35 2316166 3901039 35.377879 40.576099 36 118301889 2138660 35.401797 40.591435 37 0 4370344 35.401232 40.593682 38 0 406877 35.395058 40.589245 39 0 5167944 35.390969 40.586301 40 0 1 35.38958 40.58404 41 0 382463548 35.373476 40.572747 42 0 0 35.372356 40.572664 43 0 0 35.373263 40.572582 44 0 0 35.387305 40.582781 45 0 0 35.387668 40.583054 46 0 0 35.380566 40.576736 47 0 0 35.371169 40.571398 48 0 0 35.361866 40.564113 49 0 0 35.368519 40.569 50 0 0 35.364094 40.565925 51 0 0 35.352645 40.558996 52 0 0 35.339519 40.548175 53 0 0 35.326726 40.543088 54 0 0 35.32096 40.536691 55 0 0 35.303808 40.524199 56 0 0 35.280309 40.508981 57 0 0 35.266515 40.497023 58 0 0 35.241298 40.478277 59 0 0 35.203189 40.449788 60 0 0 35.159508 40.416407 61 0 0 35.112712 40.380853 62 0 0 35.049349 40.332854 63 0 0 34.991083 40.287308 64 0 0 34.924758 40.23627 65 0 0 34.856026 40.183262 66 0 0 34.780939 40.127134 67 0 0 34.694155 40.064288 68 0 0 34.611945 40.001052 69 0 0 34.528909 39.937137 70 0 0 34.440004 39.866393 71 0 0 34.353671 39.798266 72 0 0 34.274825 39.73515 73 0 0 34.205431 39.680154 74 0 0 34.127691 39.619046 75 0 0 34.058864 39.56453 76 0 0 33.994252 39.515517 77 0 0 33.939938 39.473664 78 0 0 33.891257 39.437309 79 0 0 33.845465 39.398759 80 0 0 33.802252 39.36309 81 0 0 33.757766 39.325515 82 0 0 33.724366 39.296023 83 0 0 33.709122 39.280827 84 0 0 33.659924 39.243221 85 0 0 33.625492 39.215431 86 0 0 33.585214 39.183231 87 0 0 33.544576 39.149301 88 0 0 33.51007 39.12153 89 0 0 33.471779 39.088286 90 0 0 33.423307 39.046172 91 0 0 33.377365 39.007226 92 0 0 33.336495 38.971423 93 0 0 33.314473 38.953338 94 0 0 33.285018 38.929904 95 0 0 33.267998 38.914397 96 0 0 33.258498 38.907497 97 0 0 33.253316 38.901531 98 0 0 33.263063 38.906932 99 0 0 33.276177 38.917808 100 0 0 33.303559 38.940226 101 0 0 33.342412 38.967888 102 0 0 33.38518 39.0014 103 0 0 33.414972 39.022065 104 0 0 33.424163 39.025429 105 0 0 33.436179 39.033983 106 0 0 33.446907 39.03986 107 0 0 33.434965 39.024825 108 0 0 33.415877 39.012677 109 0 0 33.400455 39.0024 110 0 0 33.367865 38.975509 111 0 0 33.33396 38.949968 112 0 0 33.27376 38.899987 113 0 0 33.230394 38.864826 114 0 0 33.160319 38.805905 115 0 0 33.121722 38.775368 116 0 0 33.083656 38.74609 117 0 0 33.047526 38.716486 118 0 0 33.0666 38.737798 119 0 0 33.06337 38.735195 120 0 0 33.058461 38.729717 121 0 0 33.071047 38.741416 122 0 0 33.075866 38.742303 123 0 0 33.059028 38.727436 124 0 0 33.068576 38.733829 125 0 0 33.073887 38.734565 126 0 0 33.0822 38.734043 127 0 0 33.074976 38.722029 128 0 0 33.052942 38.704725 129 0 0 33.030509 38.686389 130 0 0 32.987001 38.651148 131 0 0 32.973261 38.640451 132 0 0 32.962002 38.629041 133 0 0 32.950354 38.617658 134 0 0 32.94261 38.613929 135 0 0 32.931914 38.599891 136 0 0 32.925608 38.593555 137 0 0 32.917065 38.588398 138 0 0 32.905532 38.579252 139 0 0 32.92321 38.599371 140 0 0 32.950455 38.617443 141 0 0 32.954018 38.621357 142 0 0 32.968979 38.636188 143 0 0 32.952775 38.619043 144 0 0 32.958999 38.62076 145 0 0 32.946672 38.607585 146 0 0 32.92239 38.587767 147 0 0 32.89356 38.559264 148 0 0 32.867958 38.539891 149 0 0 32.834172 38.511055 150 0 0 32.803333 38.484998 151 0 0 32.793834 38.476358 152 0 0 32.763722 38.458969 153 0 0 32.769552 38.458689 154 0 0 32.762841 38.455698 155 0 0 32.773337 38.46318 156 0 0 32.778234 38.466335 157 0 0 32.793969 38.476906 158 0 0 32.813114 38.493185 159 0 0 32.856699 38.52819 160 0 0 32.888592 38.551097 161 0 0 32.913131 38.57092 162 0 0 32.95899 38.607659 163 0 0 32.980275 38.62526 164 0 0 32.988851 38.63194 165 0 0 33.011001 38.649318 166 0 0 33.010856 38.6457 167 0 0 32.991356 38.626119 168 0 0 32.995339 38.626581 169 0 0 32.944741 38.585887 170 0 0 32.928649 38.570235 171 0 0 32.929784 38.574653 172 0 0 32.933246 38.574097 173 0 0 32.939096 38.581141 174 0 0 32.945967 38.590003 175 0 0 32.974812 38.617288 176 0 0 32.999582 38.632658 177 0 0 33.01848 38.653344 178 0 0 33.05389 38.685079 179 0 0 33.099111 38.723431 180 0 0 33.131956 38.755194 181 0 0 33.187687 38.799655 182 0 0 33.217127 38.823524 183 0 0 33.247119 38.848245 184 0 0 33.290046 38.880667 185 0 0 33.298915 38.897358 186 0 0 33.333351 38.91898 187 0 0 33.353348 38.939814 188 0 0 33.378539 38.955511 189 0 0 33.376799 38.956992 190 0 0 33.363949 38.954285 191 0 0 33.384568 38.969455 192 0 0 33.347346 38.941296 193 0 0 33.339118 38.944506 194 0 0 33.34102 38.950693 195 0 0 33.316505 38.932153 196 0 0 33.34298 38.962785 197 0 0 33.350859 38.967721 198 0 0 33.312327 38.944109 199 0 0 33.343931 38.972116 200 0 0 33.30869 38.954771 201 0 0 33.295354 38.959042 202 0 0 33.311478 38.971585 203 0 0 33.274718 38.942456 204 0 0 33.303409 38.97417 205 0 0 33.259947 38.944656 206 0 0 33.226899 38.9298 207 0 0 33.230708 38.936701 208 0 0 33.216091 38.924194 209 0 0 33.20464 38.92596 210 0 0 33.17686 38.914026 211 0 0 33.17789 38.909826 212 0 0 33.156255 38.903025 213 0 0 33.137301 38.889456 214 0 0 33.17465 38.920915 215 0 0 33.134314 38.901477 216 0 0 33.095147 38.87089 217 0 0 33.085378 38.864835 218 0 0 33.07716 38.866457 219 0 0 33.033925 38.831614 220 0 0 32.998611 38.802861 221 0 0 33.007316 38.798247 222 0 0 32.910594 38.745955 223 0 0 32.929378 38.771072 224 0 0 32.908199 38.757121 225 0 0 32.902681 38.75554 226 0 0 32.895583 38.741836 227 0 0 32.894302 38.739983 228 0 0 32.897226 38.755578 229 0 0 32.845331 38.718981 230 0 0 32.770347 38.662186 231 0 0 32.781268 38.68465 232 0 0 32.762648 38.66088 233 0 0 32.713497 38.625845 234 0 0 32.702577 38.632471 235 0 0 32.713098 38.639117 236 0 0 32.689298 38.609674 237 0 0 32.713951 38.637406 238 0 0 32.651268 38.60555 239 0 0 32.554214 38.540159 240 0 0 32.561777 38.545189 241 0 0 32.492341 38.492057 242 0 0 32.558678 38.556613 243 0 0 32.45048 38.473012 244 0 0 32.485507 38.500138 245 0 0 32.32851 38.387232 246 0 0 32.3802 38.431364 247 0 0 32.317866 38.387432 248 0 0 32.277186 38.350548 249 0 0 32.269871 38.359916 250 0 0 32.228079 38.334738 251 0 0 32.190542 38.297673 252 0 0 32.145929 38.275546 253 0 0 32.042527 38.219408 254 0 0 32.087087 38.247371 255 0 0 32.051838 38.235897 256 0 0 31.988068 38.178766 257 0 0 32.037452 38.198107 258 0 0 31.85761 38.09346 259 0 0 31.859992 38.088843 260 0 0 31.828925 38.061888 261 0 0 31.764658 38.036451 262 0 0 31.758359 38.027014 263 0 0 31.637675 37.945377 264 0 0 31.596607 37.913745 265 0 0 31.623462 37.931659 266 0 0 31.44774 37.829665 267 0 0 31.482981 37.853842 268 0 0 31.355123 37.764096 269 0 0 31.378103 37.785336 270 0 0 31.286307 37.711805 271 0 0 31.219175 37.674575 272 0 0 31.261341 37.718229 273 0 0 31.076677 37.59015 274 0 0 30.920566 37.469754 275 0 0 30.986775 37.502112 276 0 0 30.907629 37.470962 277 0 0 30.836819 37.413358 278 0 0 30.690154 37.301797 279 0 0 30.668392 37.280515 280 0 0 30.610595 37.250845 281 0 0 30.504742 37.199306 282 0 0 30.559051 37.237532 283 0 0 30.370711 37.092732 284 0 0 30.299914 37.057865 285 0 0 30.3267 37.050656 286 0 0 30.216497 36.988286 287 0 0 30.175501 36.960124 288 0 0 30.080197 36.889371 289 0 0 30.140063 36.942087 290 0 0 30.040633 36.866005 291 0 0 29.847192 36.724046 292 0 0 29.895315 36.752154 293 0 0 29.834503 36.758037 294 0 0 29.829386 36.72147 295 0 0 29.571377 36.556286 296 0 0 29.533837 36.54263 297 0 0 29.404097 36.412149 298 0 0 29.562343 36.511318 299 0 0 29.312617 36.354605 300 0 0 29.26043 36.331486 301 0 0 29.314997 36.376005 302 0 0 29.148315 36.264238 303 0 0 29.058399 36.166272 304 0 0 29.209909 36.306649 305 0 0 28.997666 36.117671 306 0 0 28.761196 35.963691 307 0 0 28.809103 36.007053 308 0 0 28.901764 36.082106 309 0 0 28.725222 35.968273 310 0 0 28.826427 36.03835 311 0 0 28.664256 35.850433 312 0 0 28.680142 35.880603 313 0 0 28.326661 35.657567 314 0 0 28.670982 35.824621 315 0 0 28.328944 35.699236 316 0 0 28.781927 35.905739 317 0 0 28.434378 35.723756 318 0 0 28.380936 35.698098 319 0 0 28.267334 35.677049 320 0 0 28.507212 35.782051 321 0 0 28.245184 35.625073 322 0 0 28.173366 35.543664 323 0 0 28.105291 35.456975 324 0 0 28.120376 35.528479 325 0 0 28.154349 35.515588 326 0 0 27.633166 35.265135 327 0 0 27.92891 35.37941 328 0 0 27.933862 35.343327 329 0 0 28.061523 35.473958 330 0 0 28.027473 35.475458 331 0 0 27.560588 35.117911 332 0 0 27.940781 35.268282 333 0 0 28.164384 35.615931 334 0 0 27.804422 35.223356 335 0 0 27.905303 35.358586 336 0 0 28.150515 35.499656 337 0 0 27.384259 35.022377 338 0 0 28.187831 35.669312 339 0 0 27.384848 34.993939 340 0 0 28.165493 35.570423 341 0 0 27.641667 35.279167 342 0 0 28.057971 35.381643 343 0 0 27.137363 34.750916 344 0 0 28.595092 35.889571 345 0 0 28.041096 35.547945 346 0 0 28.158333 35.630556 347 0 0 27.9 35.660606 348 0 0 27.175824 34.395604 349 0 0 27.072289 34.863454 350 0 0 26.480519 34.155844 351 0 0 28.940299 35.935323 352 0 0 29 36.369048 353 0 0 26.520833 33.854167 354 0 0 28.785714 36.214286 355 0 0 29.27027 36.225225 356 0 0 27.064516 35 357 0 0 30.592593 37.358025 358 0 0 26.96 34.52 359 0 0 29.954545 36.484848 360 0 0 30.333333 37.253968 361 0 0 25.684211 32.631579 362 0 0 30.117647 36.686275 363 0 0 27.769231 35.205128 364 0 0 24.666667 34.444444 365 0 0 27.833333 35.138889 366 0 0 27.545455 35.757576 367 0 0 29.2 36.333333 368 0 0 31.3 38.3 369 0 0 28.111111 35.592593 370 0 0 30.125 36.875 371 0 0 29.285714 37.333333 372 0 0 32.333333 38.555556 373 0 0 27.6 36.4 374 0 0 28.8 36.2 375 0 0 29.4 36.733333 376 0 0 34 39.866667 377 0 0 29.4 37.066667 378 0 0 23.25 34.333333 379 0 0 31.75 38.75 380 0 0 32.25 37.75 381 0 0 26.5 34.083333 382 0 0 18.75 29 383 0 0 32.5 38 384 0 0 36 41 385 0 0 36 41 386 0 0 29 35 387 0 0 16 26 388 0 0 36 41 389 0 0 36 41 390 0 0 31 37.333333