## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5385-Z0069-CATCACTGCAACGAT/441525-L5385-Z0069-CATCACTGCAACGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5385-Z0069-CATCACTGCAACGAT/441525-L5385-Z0069-CATCACTGCAACGAT_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 03:02:06 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 999510 999510 141 141127914 141127914 135960092 135960092 126427057 126427057 0 0 0.963382 0.895833 0 0.963382 0.895833 0 423383742 423383742 416588964 416588964 401201805 401201805 375534126 375534126 0.983951 0.947608 0.886983 0.983951 0.947608 0.886983 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 1071 0 35.99343 40.995112 1 13810 0 35.982535 40.98853 2 16389 5567 35.99278 40.994014 3 41186 1507 35.979895 40.98342 4 62872 58748 35.990601 40.992434 5 129850 20291 35.995051 40.99594 6 113052 151858 35.978289 40.982537 7 220507 185743 35.98057 40.986728 8 199734 161533 35.987346 40.989891 9 262673 129385 35.958537 40.964995 10 275568 534878 35.82523 40.898557 11 319009 74491 35.887773 40.915489 12 372255 752016 35.289998 40.403449 13 361030 217414 33.86345 39.682074 14 486257 1032962 35.86119 40.913969 15 398854 406306 35.853159 40.896935 16 391887 431358 35.828884 40.851625 17 536064 1123052 35.911754 40.92806 18 576556 793969 35.673225 40.729654 19 389198 713700 35.708279 40.786176 20 553313 1003298 35.891866 40.927809 21 710064 1479213 35.787383 40.843829 22 348854 560672 35.524511 40.67626 23 1120990 1341657 35.178301 40.426501 24 622492 1299235 35.226397 40.473684 25 557342 500223 35.227251 40.475199 26 1794054 2632455 35.147839 40.406706 27 395586 949694 35.182852 40.44531 28 970853 438623 35.185704 40.449423 29 2459487 5182089 35.173671 40.436843 30 818361 43536 35.193909 40.451424 31 2417739 924273 35.183863 40.442612 32 1777437 5475151 35.168117 40.424825 33 903723 142069 35.183568 40.441006 34 2566564 2987044 35.175447 40.43811 35 2271523 3840699 35.195019 40.450265 36 115671710 2406287 35.220781 40.468566 37 0 4263911 35.212943 40.463674 38 0 416548 35.204108 40.458918 39 0 5168161 35.200234 40.454536 40 0 0 35.190062 40.445835 41 0 375534126 35.176702 40.436381 42 0 0 35.174332 40.43616 43 0 0 35.181505 40.439599 44 0 0 35.18458 40.442709 45 0 0 35.190983 40.445259 46 0 0 35.172732 40.433223 47 0 0 35.169455 40.431107 48 0 0 35.149432 40.415157 49 0 0 35.141191 40.411332 50 0 0 35.153086 40.420125 51 0 0 35.150421 40.418016 52 0 0 35.108645 40.389616 53 0 0 35.088459 40.382479 54 0 0 35.09356 40.382148 55 0 0 35.083378 40.375676 56 0 0 35.041332 40.355119 57 0 0 35.060097 40.355676 58 0 0 35.050463 40.348134 59 0 0 35.029246 40.332413 60 0 0 34.991854 40.304555 61 0 0 34.959355 40.279665 62 0 0 34.921768 40.250528 63 0 0 34.871899 40.214312 64 0 0 34.829414 40.181682 65 0 0 34.763615 40.133868 66 0 0 34.708826 40.091598 67 0 0 34.638153 40.040414 68 0 0 34.570276 39.990061 69 0 0 34.49217 39.929069 70 0 0 34.417827 39.871396 71 0 0 34.333174 39.802099 72 0 0 34.239344 39.728537 73 0 0 34.151029 39.65749 74 0 0 34.063106 39.588009 75 0 0 33.97788 39.521151 76 0 0 33.900109 39.46039 77 0 0 33.812162 39.393918 78 0 0 33.746568 39.341623 79 0 0 33.678254 39.286932 80 0 0 33.613107 39.232747 81 0 0 33.564135 39.194498 82 0 0 33.512528 39.151575 83 0 0 33.469989 39.11539 84 0 0 33.435377 39.091014 85 0 0 33.398629 39.055948 86 0 0 33.367025 39.029604 87 0 0 33.325577 38.998141 88 0 0 33.29001 38.964903 89 0 0 33.259489 38.937835 90 0 0 33.224973 38.907047 91 0 0 33.188881 38.875106 92 0 0 33.153616 38.844044 93 0 0 33.121904 38.81593 94 0 0 33.089208 38.78718 95 0 0 33.061276 38.765469 96 0 0 33.061863 38.763211 97 0 0 33.042051 38.749672 98 0 0 33.024454 38.734553 99 0 0 33.046193 38.75118 100 0 0 33.060479 38.760162 101 0 0 33.0822 38.778323 102 0 0 33.122713 38.80994 103 0 0 33.138303 38.819719 104 0 0 33.171954 38.845386 105 0 0 33.194537 38.86354 106 0 0 33.208174 38.869894 107 0 0 33.20925 38.871839 108 0 0 33.207541 38.866419 109 0 0 33.200472 38.862304 110 0 0 33.174767 38.841415 111 0 0 33.1574 38.830307 112 0 0 33.116776 38.794872 113 0 0 33.061038 38.747257 114 0 0 33.013831 38.704468 115 0 0 32.959911 38.66454 116 0 0 32.92942 38.640234 117 0 0 32.917471 38.634484 118 0 0 32.898319 38.61917 119 0 0 32.914605 38.637713 120 0 0 32.926679 38.645558 121 0 0 32.943003 38.65655 122 0 0 32.953033 38.663886 123 0 0 32.953782 38.663961 124 0 0 32.962672 38.670405 125 0 0 32.986768 38.68389 126 0 0 33.003514 38.691949 127 0 0 33.018009 38.700124 128 0 0 32.994965 38.683813 129 0 0 32.987911 38.67127 130 0 0 32.964823 38.651345 131 0 0 32.947078 38.640232 132 0 0 32.947072 38.635965 133 0 0 32.946832 38.637977 134 0 0 32.953982 38.63862 135 0 0 32.939736 38.622909 136 0 0 32.927218 38.617636 137 0 0 32.902479 38.598357 138 0 0 32.900041 38.597136 139 0 0 32.919899 38.613408 140 0 0 32.940316 38.630785 141 0 0 32.97234 38.657567 142 0 0 32.995324 38.675648 143 0 0 33.000607 38.681024 144 0 0 32.99409 38.669608 145 0 0 32.990707 38.663905 146 0 0 32.977106 38.652777 147 0 0 32.939794 38.621592 148 0 0 32.904893 38.59358 149 0 0 32.85939 38.550745 150 0 0 32.850897 38.54882 151 0 0 32.807897 38.508965 152 0 0 32.784376 38.490906 153 0 0 32.763134 38.477885 154 0 0 32.76433 38.476145 155 0 0 32.76469 38.476575 156 0 0 32.763477 38.471886 157 0 0 32.772323 38.48119 158 0 0 32.808597 38.507329 159 0 0 32.803075 38.501711 160 0 0 32.84529 38.536554 161 0 0 32.858055 38.546642 162 0 0 32.886038 38.565892 163 0 0 32.907444 38.586884 164 0 0 32.896746 38.578507 165 0 0 32.895035 38.578724 166 0 0 32.884974 38.565196 167 0 0 32.856386 38.534192 168 0 0 32.807374 38.490756 169 0 0 32.76166 38.450375 170 0 0 32.703598 38.401487 171 0 0 32.669938 38.374071 172 0 0 32.654321 38.359672 173 0 0 32.6609 38.368771 174 0 0 32.652165 38.35594 175 0 0 32.62859 38.342138 176 0 0 32.664465 38.376744 177 0 0 32.697401 38.400992 178 0 0 32.726204 38.419634 179 0 0 32.771998 38.461461 180 0 0 32.798858 38.485538 181 0 0 32.854242 38.528176 182 0 0 32.917553 38.589009 183 0 0 32.934607 38.591799 184 0 0 32.985389 38.637872 185 0 0 33.040842 38.681726 186 0 0 33.0824 38.712721 187 0 0 33.094172 38.725326 188 0 0 33.118125 38.747169 189 0 0 33.138899 38.756673 190 0 0 33.135223 38.766311 191 0 0 33.114894 38.747214 192 0 0 33.07845 38.72504 193 0 0 33.055945 38.711959 194 0 0 33.037735 38.701485 195 0 0 33.009224 38.686291 196 0 0 32.989474 38.678938 197 0 0 33.017328 38.704245 198 0 0 32.979553 38.679286 199 0 0 32.959765 38.67272 200 0 0 32.934836 38.661479 201 0 0 32.908603 38.651929 202 0 0 32.900322 38.648249 203 0 0 32.88778 38.650553 204 0 0 32.82813 38.614618 205 0 0 32.846896 38.636696 206 0 0 32.810318 38.616739 207 0 0 32.798971 38.611854 208 0 0 32.732104 38.571942 209 0 0 32.734621 38.572912 210 0 0 32.775368 38.598723 211 0 0 32.706855 38.551285 212 0 0 32.708511 38.564146 213 0 0 32.673589 38.542466 214 0 0 32.637084 38.515828 215 0 0 32.622682 38.513145 216 0 0 32.60672 38.498092 217 0 0 32.571371 38.476419 218 0 0 32.546696 38.466857 219 0 0 32.591716 38.502044 220 0 0 32.512151 38.448626 221 0 0 32.46905 38.418457 222 0 0 32.481986 38.430585 223 0 0 32.472662 38.429237 224 0 0 32.405179 38.370118 225 0 0 32.43573 38.403822 226 0 0 32.389156 38.376852 227 0 0 32.43583 38.41054 228 0 0 32.371308 38.363409 229 0 0 32.308774 38.319908 230 0 0 32.317037 38.335771 231 0 0 32.242118 38.27706 232 0 0 32.180477 38.22358 233 0 0 32.187587 38.237987 234 0 0 32.155253 38.223995 235 0 0 32.125829 38.210072 236 0 0 32.133679 38.20124 237 0 0 32.119265 38.201119 238 0 0 32.023739 38.145933 239 0 0 32.081459 38.186713 240 0 0 32.096866 38.198125 241 0 0 32.045695 38.162434 242 0 0 32.036402 38.150521 243 0 0 32.015719 38.14884 244 0 0 31.980913 38.119216 245 0 0 31.945581 38.104598 246 0 0 31.866598 38.039129 247 0 0 31.91693 38.090822 248 0 0 31.93562 38.098593 249 0 0 31.842537 38.041234 250 0 0 31.820249 38.018477 251 0 0 31.724678 37.960786 252 0 0 31.659606 37.913054 253 0 0 31.593961 37.870825 254 0 0 31.66277 37.910108 255 0 0 31.56561 37.858683 256 0 0 31.515019 37.829946 257 0 0 31.567728 37.86865 258 0 0 31.567933 37.880415 259 0 0 31.481172 37.833169 260 0 0 31.419768 37.78348 261 0 0 31.371396 37.736395 262 0 0 31.235196 37.676027 263 0 0 31.186594 37.617889 264 0 0 31.142066 37.597463 265 0 0 31.195622 37.635118 266 0 0 31.196801 37.620813 267 0 0 31.173987 37.647423 268 0 0 31.017801 37.511499 269 0 0 31.008955 37.479045 270 0 0 30.842344 37.406563 271 0 0 30.907454 37.45379 272 0 0 30.828383 37.408574 273 0 0 30.766592 37.33065 274 0 0 30.628971 37.254532 275 0 0 30.614209 37.234247 276 0 0 30.831967 37.391841 277 0 0 30.279288 37.010848 278 0 0 30.463667 37.157762 279 0 0 30.389116 37.08711 280 0 0 30.38812 37.089514 281 0 0 30.095503 36.899147 282 0 0 30.084054 36.897829 283 0 0 30.251423 37.04062 284 0 0 30.053841 36.900434 285 0 0 30.141274 36.949566 286 0 0 29.79126 36.694715 287 0 0 29.650943 36.642558 288 0 0 29.640434 36.603976 289 0 0 29.694832 36.579747 290 0 0 29.522539 36.47261 291 0 0 29.669935 36.645455 292 0 0 29.260879 36.345241 293 0 0 29.351388 36.382423 294 0 0 29.339522 36.456718 295 0 0 29.089226 36.200738 296 0 0 29.198146 36.285321 297 0 0 29.042653 36.140962 298 0 0 29.094217 36.205901 299 0 0 29.018777 36.155714 300 0 0 29.080669 36.169605 301 0 0 29.024168 36.152647 302 0 0 28.852475 36.042354 303 0 0 28.701633 35.909459 304 0 0 28.53172 35.805647 305 0 0 28.671869 35.917284 306 0 0 28.55097 35.861467 307 0 0 28.516271 35.856494 308 0 0 28.343823 35.646939 309 0 0 28.802005 36.000334 310 0 0 28.505336 35.818036 311 0 0 28.457569 35.780008 312 0 0 28.514321 35.806351 313 0 0 28.331785 35.570007 314 0 0 28.415217 35.75628 315 0 0 28.059608 35.420915 316 0 0 28.468484 35.808631 317 0 0 28.093492 35.509624 318 0 0 28.752731 35.935452 319 0 0 28.001098 35.386023 320 0 0 28.470937 35.713325 321 0 0 28.409623 35.697443 322 0 0 28.666187 35.929496 323 0 0 28.567863 35.885595 324 0 0 28.598291 35.850712 325 0 0 28.29368 35.652416 326 0 0 28.535787 35.707566 327 0 0 27.334071 34.980826 328 0 0 28.110577 35.523237 329 0 0 27.92973 35.257658 330 0 0 28.051051 35.532533 331 0 0 27.087719 34.817544 332 0 0 27.838583 35.577428 333 0 0 28.083333 35.372807 334 0 0 28.40099 35.831683 335 0 0 27.940217 35.384058 336 0 0 27.460606 35.381818 337 0 0 27.92053 35.373068 338 0 0 27.929687 35.619792 339 0 0 29.543103 36.514368 340 0 0 28.971154 36.448718 341 0 0 26.709677 34.802867 342 0 0 28.175 35.8375 343 0 0 26.384615 34.051282 344 0 0 28.962963 36.092593 345 0 0 28.306122 35.816327 346 0 0 25.473684 34.894737 347 0 0 24.969697 33.343434 348 0 0 29.533333 36.411111 349 0 0 27.090909 34.833333 350 0 0 25.894737 35.350877 351 0 0 27.944444 35.648148 352 0 0 28 35.880952 353 0 0 22.75 32.333333 354 0 0 28.888889 35.666667 355 0 0 26.375 34.041667 356 0 0 36 41 357 0 0 32.25 39 358 0 0 33.666667 39 359 0 0 25 32.5 360 0 0 30.5 36.5 361 0 0 27 33.666667 362 0 0 36 41 363 0 0 26 36 364 0 0 36 41 365 0 0 32 37.666667 366 0 0 21 30.333333 367 0 0 12 24.666667 368 0 0 29 37 369 0 0 18 33.333333 370 0 0 20 28.666667 371 0 0 21 34.333333 372 0 0 31 38 373 0 0 21 34.333333 374 0 0 31 37.333333 375 0 0 36 40.333333 376 0 0 32 38.666667 377 0 0 31 38