## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5282-Z0025-CTCGAGATTGATGAT/441525-L5282-Z0025-CTCGAGATTGATGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5282-Z0025-CTCGAGATTGATGAT/441525-L5282-Z0025-CTCGAGATTGATGAT_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 03:02:19 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 1000132 1000132 181 181307155 181307155 176602516 176602516 166982220 166982220 0 0 0.974052 0.920991 0 0.974052 0.920991 0 543921465 543921465 537842985 537842985 522754922 522754922 496320209 496320209 0.988825 0.961085 0.912485 0.988825 0.961085 0.912485 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 1065 0 35.994595 40.995906 1 14257 0 35.984575 40.990027 2 17013 6646 35.993237 40.994561 3 41220 1755 35.981404 40.985015 4 61019 57546 35.990564 40.992363 5 124643 16047 35.9953 40.996183 6 96352 149182 35.972258 40.978594 7 205128 173550 35.98118 40.986833 8 166265 150506 35.988085 40.990257 9 236017 112278 35.93554 40.945966 10 245038 488954 35.915861 40.945042 11 286651 67531 35.949312 40.96362 12 327704 681043 35.620011 40.681812 13 314954 192841 34.768266 40.240326 14 446631 920052 35.90532 40.944253 15 369379 367133 35.728215 40.814523 16 346711 366390 35.739091 40.770596 17 493506 986764 35.910054 40.926599 18 533991 704897 35.687938 40.753479 19 377095 635365 35.818463 40.868433 20 570193 915991 35.941794 40.960098 21 662246 1370367 35.844469 40.886692 22 367081 512293 35.659369 40.767176 23 1208213 1447738 35.414263 40.599448 24 597358 1232066 35.479033 40.641804 25 538205 509589 35.463758 40.635338 26 1867005 2635886 35.414204 40.597049 27 362873 976693 35.438814 40.622297 28 953674 426145 35.443596 40.624541 29 2493448 5061295 35.434227 40.616364 30 842483 54904 35.431449 40.615016 31 2526967 1083523 35.42905 40.6121 32 1912568 5238549 35.425631 40.607539 33 953095 158998 35.423615 40.609417 34 2715998 3183108 35.41986 40.607421 35 2560634 3760118 35.442265 40.62157 36 155470475 2680095 35.46168 40.634739 37 0 4263393 35.450552 40.628807 38 0 606644 35.446758 40.626967 39 0 5405381 35.444132 40.62443 40 0 2 35.43693 40.618582 41 0 496320207 35.426143 40.610058 42 0 0 35.415296 40.603892 43 0 0 35.424373 40.608879 44 0 0 35.432015 40.614402 45 0 0 35.4279 40.610795 46 0 0 35.424493 40.609167 47 0 0 35.417669 40.604215 48 0 0 35.406801 40.596595 49 0 0 35.406881 40.597658 50 0 0 35.407846 40.598651 51 0 0 35.410236 40.598043 52 0 0 35.389748 40.584975 53 0 0 35.384988 40.585482 54 0 0 35.380547 40.580959 55 0 0 35.375699 40.576731 56 0 0 35.366288 40.57327 57 0 0 35.372612 40.574692 58 0 0 35.368834 40.570606 59 0 0 35.364635 40.568005 60 0 0 35.351154 40.556972 61 0 0 35.342535 40.551068 62 0 0 35.328579 40.540207 63 0 0 35.309794 40.525298 64 0 0 35.29447 40.515681 65 0 0 35.279071 40.503228 66 0 0 35.266093 40.493116 67 0 0 35.236672 40.473808 68 0 0 35.216436 40.456649 69 0 0 35.196842 40.442689 70 0 0 35.165382 40.417604 71 0 0 35.136902 40.396975 72 0 0 35.104226 40.370647 73 0 0 35.074828 40.346905 74 0 0 35.046869 40.322929 75 0 0 35.015128 40.299085 76 0 0 34.980254 40.271369 77 0 0 34.944567 40.244405 78 0 0 34.903712 40.213329 79 0 0 34.874476 40.190639 80 0 0 34.840251 40.161895 81 0 0 34.806235 40.133878 82 0 0 34.774516 40.110979 83 0 0 34.743615 40.085046 84 0 0 34.718985 40.064515 85 0 0 34.693968 40.046891 86 0 0 34.672505 40.028625 87 0 0 34.647702 40.009564 88 0 0 34.626939 39.991308 89 0 0 34.604827 39.973107 90 0 0 34.586831 39.956931 91 0 0 34.562056 39.935572 92 0 0 34.54533 39.921301 93 0 0 34.532364 39.908733 94 0 0 34.518451 39.895964 95 0 0 34.506342 39.887345 96 0 0 34.491736 39.874536 97 0 0 34.477441 39.863495 98 0 0 34.484113 39.866909 99 0 0 34.483728 39.866167 100 0 0 34.480333 39.862784 101 0 0 34.486641 39.866921 102 0 0 34.495917 39.873464 103 0 0 34.497093 39.87488 104 0 0 34.506052 39.879979 105 0 0 34.510891 39.881349 106 0 0 34.515194 39.886312 107 0 0 34.509867 39.882143 108 0 0 34.529143 39.896874 109 0 0 34.526877 39.894032 110 0 0 34.512719 39.88494 111 0 0 34.501882 39.874328 112 0 0 34.487663 39.862571 113 0 0 34.456354 39.83742 114 0 0 34.438158 39.819232 115 0 0 34.417354 39.801978 116 0 0 34.39979 39.789391 117 0 0 34.38329 39.776627 118 0 0 34.385563 39.781795 119 0 0 34.372779 39.771798 120 0 0 34.372705 39.772123 121 0 0 34.368824 39.769763 122 0 0 34.373332 39.76934 123 0 0 34.362132 39.759757 124 0 0 34.361973 39.759636 125 0 0 34.37188 39.765833 126 0 0 34.366867 39.760372 127 0 0 34.373887 39.764522 128 0 0 34.377581 39.76772 129 0 0 34.377704 39.769028 130 0 0 34.380912 39.770369 131 0 0 34.363294 39.756263 132 0 0 34.358857 39.75197 133 0 0 34.355033 39.749249 134 0 0 34.351027 39.742494 135 0 0 34.340095 39.732365 136 0 0 34.333258 39.72599 137 0 0 34.325943 39.720888 138 0 0 34.312626 39.710753 139 0 0 34.30519 39.706111 140 0 0 34.317147 39.719333 141 0 0 34.335771 39.73339 142 0 0 34.329209 39.726764 143 0 0 34.327776 39.728339 144 0 0 34.31014 39.712534 145 0 0 34.304555 39.704787 146 0 0 34.27773 39.68211 147 0 0 34.253497 39.662603 148 0 0 34.235716 39.645258 149 0 0 34.211078 39.626678 150 0 0 34.179179 39.601832 151 0 0 34.160804 39.588142 152 0 0 34.136108 39.569451 153 0 0 34.124296 39.558293 154 0 0 34.103362 39.541454 155 0 0 34.086024 39.527853 156 0 0 34.076123 39.519112 157 0 0 34.063315 39.504362 158 0 0 34.046406 39.491297 159 0 0 34.045748 39.491317 160 0 0 34.04269 39.487428 161 0 0 34.045021 39.488408 162 0 0 34.039649 39.486116 163 0 0 34.024586 39.474889 164 0 0 34.019041 39.470683 165 0 0 33.987513 39.444127 166 0 0 33.949849 39.411056 167 0 0 33.90794 39.375249 168 0 0 33.863075 39.334203 169 0 0 33.778174 39.262606 170 0 0 33.726494 39.217046 171 0 0 33.669549 39.170773 172 0 0 33.620525 39.131103 173 0 0 33.584793 39.103765 174 0 0 33.552438 39.07722 175 0 0 33.525161 39.052251 176 0 0 33.502892 39.035126 177 0 0 33.512274 39.038709 178 0 0 33.488061 39.023266 179 0 0 33.482914 39.016859 180 0 0 33.490795 39.021983 181 0 0 33.502319 39.032541 182 0 0 33.526645 39.048746 183 0 0 33.541716 39.064237 184 0 0 33.562417 39.081853 185 0 0 33.600861 39.113002 186 0 0 33.61001 39.118679 187 0 0 33.62616 39.132169 188 0 0 33.619543 39.125244 189 0 0 33.638126 39.140768 190 0 0 33.642218 39.142777 191 0 0 33.641651 39.143938 192 0 0 33.609877 39.121132 193 0 0 33.609325 39.127025 194 0 0 33.57861 39.108384 195 0 0 33.550376 39.089141 196 0 0 33.547831 39.091359 197 0 0 33.53306 39.084758 198 0 0 33.533035 39.085373 199 0 0 33.511103 39.075678 200 0 0 33.502998 39.074611 201 0 0 33.484172 39.068871 202 0 0 33.440951 39.041957 203 0 0 33.41528 39.029269 204 0 0 33.386647 39.012668 205 0 0 33.344806 38.98903 206 0 0 33.315805 38.971079 207 0 0 33.303967 38.971132 208 0 0 33.289122 38.961455 209 0 0 33.240585 38.933155 210 0 0 33.223524 38.927804 211 0 0 33.186606 38.903971 212 0 0 33.146786 38.881562 213 0 0 33.112452 38.859234 214 0 0 33.094031 38.85015 215 0 0 33.068587 38.83654 216 0 0 33.041297 38.820097 217 0 0 33.026782 38.812393 218 0 0 33.024851 38.812694 219 0 0 32.970745 38.775837 220 0 0 32.966517 38.775665 221 0 0 32.937205 38.761108 222 0 0 32.906357 38.735385 223 0 0 32.895255 38.731274 224 0 0 32.851257 38.702519 225 0 0 32.845555 38.698962 226 0 0 32.827822 38.688002 227 0 0 32.782859 38.664118 228 0 0 32.777051 38.653085 229 0 0 32.731838 38.62702 230 0 0 32.719135 38.616092 231 0 0 32.6871 38.596494 232 0 0 32.689816 38.611427 233 0 0 32.646634 38.576646 234 0 0 32.626502 38.565198 235 0 0 32.610355 38.558113 236 0 0 32.588258 38.55156 237 0 0 32.531155 38.509138 238 0 0 32.583147 38.546589 239 0 0 32.535936 38.519233 240 0 0 32.500177 38.494739 241 0 0 32.449704 38.452625 242 0 0 32.441914 38.453396 243 0 0 32.385141 38.418295 244 0 0 32.374349 38.408892 245 0 0 32.331276 38.380304 246 0 0 32.298924 38.372324 247 0 0 32.29868 38.362723 248 0 0 32.199001 38.30039 249 0 0 32.184211 38.29617 250 0 0 32.208685 38.305718 251 0 0 32.170723 38.288963 252 0 0 32.130578 38.256516 253 0 0 32.081889 38.234064 254 0 0 32.025532 38.200447 255 0 0 31.993455 38.178854 256 0 0 32.007224 38.184126 257 0 0 31.966176 38.165481 258 0 0 31.960764 38.168906 259 0 0 31.85315 38.084592 260 0 0 31.819064 38.071413 261 0 0 31.829294 38.093272 262 0 0 31.768533 38.043935 263 0 0 31.71281 38.007639 264 0 0 31.704768 38.008943 265 0 0 31.621635 37.952284 266 0 0 31.544736 37.895624 267 0 0 31.492763 37.849792 268 0 0 31.490135 37.864748 269 0 0 31.447084 37.834373 270 0 0 31.366708 37.775561 271 0 0 31.359264 37.781518 272 0 0 31.278331 37.716118 273 0 0 31.258871 37.715648 274 0 0 31.193911 37.674091 275 0 0 31.10244 37.621087 276 0 0 31.05723 37.581145 277 0 0 31.033421 37.560308 278 0 0 30.921653 37.48224 279 0 0 30.90421 37.482338 280 0 0 30.774929 37.392784 281 0 0 30.732518 37.353188 282 0 0 30.672986 37.302475 283 0 0 30.575124 37.247764 284 0 0 30.497146 37.206692 285 0 0 30.390241 37.111519 286 0 0 30.383192 37.121652 287 0 0 30.317438 37.072049 288 0 0 30.187778 36.974605 289 0 0 30.17244 36.964794 290 0 0 30.140292 36.944422 291 0 0 30.089896 36.926286 292 0 0 30.027579 36.877247 293 0 0 29.955771 36.810351 294 0 0 29.83327 36.726466 295 0 0 29.831427 36.740941 296 0 0 29.754312 36.678815 297 0 0 29.661656 36.621803 298 0 0 29.678544 36.629263 299 0 0 29.620438 36.570631 300 0 0 29.509939 36.523982 301 0 0 29.487981 36.48488 302 0 0 29.469527 36.479332 303 0 0 29.431526 36.451712 304 0 0 29.409435 36.431733 305 0 0 29.413065 36.457948 306 0 0 29.361765 36.406761 307 0 0 29.236077 36.312042 308 0 0 29.211657 36.291056 309 0 0 29.232563 36.307104 310 0 0 29.127401 36.217783 311 0 0 29.171269 36.252059 312 0 0 29.005605 36.138526 313 0 0 29.093602 36.237788 314 0 0 29.135441 36.241005 315 0 0 29.065827 36.201601 316 0 0 29.025467 36.152636 317 0 0 28.950884 36.112762 318 0 0 29.118867 36.185423 319 0 0 28.928173 36.064115 320 0 0 28.851793 36.055248 321 0 0 28.706468 35.912527 322 0 0 28.700938 35.890349 323 0 0 28.683465 35.881585 324 0 0 28.725428 35.929359 325 0 0 28.581461 35.847846 326 0 0 28.700251 35.924725 327 0 0 28.863089 36.049088 328 0 0 28.638031 35.894203 329 0 0 28.753237 36.018643 330 0 0 28.896966 36.096833 331 0 0 28.907088 36.037995 332 0 0 28.991486 36.101336 333 0 0 28.59802 35.901254 334 0 0 28.503308 35.736068 335 0 0 28.684132 35.814632 336 0 0 28.349391 35.749539 337 0 0 28.518587 35.775093 338 0 0 28.504821 35.726354 339 0 0 28.536623 35.831406 340 0 0 28.936632 36.040799 341 0 0 28.8154 35.988154 342 0 0 29.18925 36.312057 343 0 0 28.155696 35.478903 344 0 0 28.838983 36.01742 345 0 0 28.169628 35.647281 346 0 0 27.974074 35.612346 347 0 0 28.596195 36.075405 348 0 0 28.477218 35.59952 349 0 0 28.185393 35.579588 350 0 0 27.848185 35.313531 351 0 0 28.118519 35.532099 352 0 0 29.12766 36.285106 353 0 0 28.207729 35.673108 354 0 0 28.287293 35.769797 355 0 0 27.807453 35.134576 356 0 0 29.09589 36.141553 357 0 0 29.322835 36.498688 358 0 0 29.166667 36.33642 359 0 0 28.217822 35.953795 360 0 0 28.206522 35.608696 361 0 0 28.22619 35.84127 362 0 0 27.987013 35.316017 363 0 0 29.2 36.419048 364 0 0 29.15625 36.119792 365 0 0 27.389831 35.254237 366 0 0 28.714286 35.85119 367 0 0 27.375 34.638889 368 0 0 26.634146 34.398374 369 0 0 31.176471 38.107843 370 0 0 29.65625 36.354167 371 0 0 28.774194 36.150538 372 0 0 29.125 35.916667 373 0 0 29.285714 36.015873 374 0 0 29.588235 36.431373 375 0 0 26.153846 34.820513 376 0 0 31.5 37.916667 377 0 0 27.636364 34.606061 378 0 0 27 34.133333 379 0 0 26.75 35.541667 380 0 0 30.857143 37.47619 381 0 0 26.333333 34.055556 382 0 0 23.4 32.333333 383 0 0 22.75 32.666667 384 0 0 32.333333 39 385 0 0 27.5 34.833333 386 0 0 31.5 38 387 0 0 25 33.666667 388 0 0 16.5 24.833333 389 0 0 32.5 38 390 0 0 36 41