## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5415-Z0111-CTTATCTGATCTGAT/441525-L5415-Z0111-CTTATCTGATCTGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5415-Z0111-CTTATCTGATCTGAT/441525-L5415-Z0111-CTTATCTGATCTGAT_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 02:54:29 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 1001140 1001140 128 128642114 128642114 123489196 123489196 114183220 114183220 0 0 0.959944 0.887604 0 0.959944 0.887604 0 385926342 385926342 379093660 379093660 364067121 364067121 339376369 339376369 0.982295 0.943359 0.879381 0.982295 0.943359 0.879381 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 1033 0 35.99518 40.996439 1 12511 0 35.988159 40.992218 2 15043 5019 35.994571 40.995379 3 38713 1383 35.981883 40.985328 4 61340 54322 35.990562 40.992519 5 123175 20014 35.995172 40.995989 6 117076 140698 35.974964 40.979457 7 212162 175933 35.98166 40.987332 8 203170 158560 35.990544 40.992307 9 256781 124569 35.960626 40.966994 10 271003 533801 35.890777 40.933146 11 316830 70297 35.929132 40.948074 12 374270 746799 35.232232 40.351453 13 366113 227935 33.745634 39.599362 14 489942 1048873 35.899378 40.938759 15 393406 400839 35.838121 40.885601 16 403552 460623 35.80513 40.826728 17 538874 1159166 35.895256 40.911017 18 579536 777871 35.714342 40.765678 19 378388 725980 35.707776 40.786119 20 528583 1018128 35.88639 40.927449 21 690886 1439961 35.814165 40.864754 22 330504 567061 35.557117 40.693142 23 1076399 1248854 35.211578 40.449073 24 595008 1243847 35.203905 40.456635 25 544372 476764 35.218659 40.469044 26 1774428 2611477 35.142486 40.408923 27 375208 893543 35.152395 40.422948 28 949197 398733 35.171916 40.437238 29 2441391 5128171 35.166978 40.432079 30 761200 40737 35.168558 40.432963 31 2300920 830651 35.155606 40.42342 32 1642363 5462855 35.142165 40.410402 33 845206 131538 35.1471 40.414549 34 2447188 2694531 35.139798 40.410923 35 2163645 3822551 35.155834 40.422007 36 104022698 2193136 35.182398 40.440584 37 0 4200268 35.182336 40.441831 38 0 369129 35.173736 40.435991 39 0 4945356 35.169964 40.43322 40 0 0 35.15792 40.424858 41 0 339376369 35.145628 40.413848 42 0 0 35.136995 40.408337 43 0 0 35.14271 40.411654 44 0 0 35.149832 40.416709 45 0 0 35.151443 40.418867 46 0 0 35.137225 40.407909 47 0 0 35.132629 40.404887 48 0 0 35.119805 40.395942 49 0 0 35.116705 40.39387 50 0 0 35.112755 40.391848 51 0 0 35.112327 40.390953 52 0 0 35.068801 40.360473 53 0 0 35.050217 40.348167 54 0 0 35.046741 40.341297 55 0 0 35.018398 40.321358 56 0 0 34.987782 40.302851 57 0 0 34.995839 40.305871 58 0 0 34.960982 40.278239 59 0 0 34.918003 40.248317 60 0 0 34.881057 40.227196 61 0 0 34.846993 40.199032 62 0 0 34.796678 40.159694 63 0 0 34.758376 40.130506 64 0 0 34.691909 40.08081 65 0 0 34.620366 40.028055 66 0 0 34.568569 39.98897 67 0 0 34.500725 39.940714 68 0 0 34.418229 39.879609 69 0 0 34.326251 39.80833 70 0 0 34.219221 39.725978 71 0 0 34.112333 39.640805 72 0 0 33.994254 39.544125 73 0 0 33.872055 39.446691 74 0 0 33.746215 39.345425 75 0 0 33.632969 39.257865 76 0 0 33.51016 39.160193 77 0 0 33.404899 39.082289 78 0 0 33.297054 39.000008 79 0 0 33.188624 38.916172 80 0 0 33.085388 38.833561 81 0 0 33.004883 38.770045 82 0 0 32.943195 38.714906 83 0 0 32.881896 38.663408 84 0 0 32.83719 38.626985 85 0 0 32.795343 38.589934 86 0 0 32.74204 38.542924 87 0 0 32.694545 38.50796 88 0 0 32.64584 38.465152 89 0 0 32.594194 38.419091 90 0 0 32.552916 38.384133 91 0 0 32.506201 38.339151 92 0 0 32.474449 38.310178 93 0 0 32.423394 38.265943 94 0 0 32.397913 38.245929 95 0 0 32.361356 38.213997 96 0 0 32.34512 38.202139 97 0 0 32.339914 38.194726 98 0 0 32.334909 38.187746 99 0 0 32.366612 38.215104 100 0 0 32.405365 38.24348 101 0 0 32.446429 38.27449 102 0 0 32.489968 38.30895 103 0 0 32.53837 38.346192 104 0 0 32.564408 38.362665 105 0 0 32.599983 38.387937 106 0 0 32.606862 38.388167 107 0 0 32.616001 38.394787 108 0 0 32.60161 38.384619 109 0 0 32.593536 38.375265 110 0 0 32.562802 38.353281 111 0 0 32.521184 38.320982 112 0 0 32.476155 38.281778 113 0 0 32.409517 38.227455 114 0 0 32.343977 38.174184 115 0 0 32.30337 38.144148 116 0 0 32.274066 38.121031 117 0 0 32.268575 38.117643 118 0 0 32.249396 38.102445 119 0 0 32.262601 38.12221 120 0 0 32.277885 38.131537 121 0 0 32.308593 38.154144 122 0 0 32.314026 38.15857 123 0 0 32.341111 38.177558 124 0 0 32.375125 38.198426 125 0 0 32.408404 38.221501 126 0 0 32.429602 38.236021 127 0 0 32.416695 38.21794 128 0 0 32.424575 38.221755 129 0 0 32.389454 38.191323 130 0 0 32.3644 38.173798 131 0 0 32.363653 38.168991 132 0 0 32.371045 38.171477 133 0 0 32.342409 38.14633 134 0 0 32.338837 38.147485 135 0 0 32.344978 38.147692 136 0 0 32.325978 38.131593 137 0 0 32.310412 38.118119 138 0 0 32.326369 38.135848 139 0 0 32.336196 38.141872 140 0 0 32.388829 38.184853 141 0 0 32.411225 38.198114 142 0 0 32.448693 38.233373 143 0 0 32.454385 38.23894 144 0 0 32.444021 38.227269 145 0 0 32.445386 38.219459 146 0 0 32.415525 38.196876 147 0 0 32.378861 38.16104 148 0 0 32.346099 38.137646 149 0 0 32.30327 38.096086 150 0 0 32.300404 38.098403 151 0 0 32.234586 38.043938 152 0 0 32.214167 38.031186 153 0 0 32.220639 38.038441 154 0 0 32.192078 38.014463 155 0 0 32.23109 38.046739 156 0 0 32.254524 38.058997 157 0 0 32.266443 38.075576 158 0 0 32.306352 38.102851 159 0 0 32.342359 38.126196 160 0 0 32.385841 38.162708 161 0 0 32.402091 38.180238 162 0 0 32.445281 38.212444 163 0 0 32.492125 38.24832 164 0 0 32.506439 38.253206 165 0 0 32.512941 38.262139 166 0 0 32.534789 38.270458 167 0 0 32.468517 38.215362 168 0 0 32.424867 38.175642 169 0 0 32.407226 38.157562 170 0 0 32.350315 38.116067 171 0 0 32.347147 38.10766 172 0 0 32.352998 38.120123 173 0 0 32.357502 38.123091 174 0 0 32.349041 38.118814 175 0 0 32.365758 38.134689 176 0 0 32.416033 38.177018 177 0 0 32.466131 38.215219 178 0 0 32.507179 38.252667 179 0 0 32.567427 38.301202 180 0 0 32.640381 38.365174 181 0 0 32.651663 38.376539 182 0 0 32.695238 38.418472 183 0 0 32.757136 38.464916 184 0 0 32.782182 38.491624 185 0 0 32.807805 38.515486 186 0 0 32.845395 38.539727 187 0 0 32.902267 38.580221 188 0 0 32.877114 38.571717 189 0 0 32.874757 38.572847 190 0 0 32.931536 38.616378 191 0 0 32.889766 38.575655 192 0 0 32.865954 38.564241 193 0 0 32.816597 38.536472 194 0 0 32.805458 38.532577 195 0 0 32.789896 38.525142 196 0 0 32.80028 38.546337 197 0 0 32.816785 38.556665 198 0 0 32.772312 38.534932 199 0 0 32.805058 38.554694 200 0 0 32.798633 38.561335 201 0 0 32.804061 38.58093 202 0 0 32.7935 38.576672 203 0 0 32.768362 38.567362 204 0 0 32.756998 38.559809 205 0 0 32.755807 38.564558 206 0 0 32.72018 38.55654 207 0 0 32.721463 38.553975 208 0 0 32.618864 38.479322 209 0 0 32.666868 38.526693 210 0 0 32.699705 38.544843 211 0 0 32.669511 38.51794 212 0 0 32.578104 38.470783 213 0 0 32.602452 38.497045 214 0 0 32.484023 38.421819 215 0 0 32.503249 38.431513 216 0 0 32.526645 38.458832 217 0 0 32.461988 38.397907 218 0 0 32.50122 38.437258 219 0 0 32.494547 38.426436 220 0 0 32.42761 38.398703 221 0 0 32.344005 38.337325 222 0 0 32.355576 38.35943 223 0 0 32.386894 38.36715 224 0 0 32.384369 38.355778 225 0 0 32.386449 38.359741 226 0 0 32.330322 38.33695 227 0 0 32.318324 38.313369 228 0 0 32.34507 38.357991 229 0 0 32.316891 38.285865 230 0 0 32.276758 38.295887 231 0 0 32.341685 38.328619 232 0 0 32.194375 38.246652 233 0 0 32.197737 38.236796 234 0 0 32.075693 38.182638 235 0 0 32.072085 38.170498 236 0 0 32.212728 38.267098 237 0 0 32.137088 38.1975 238 0 0 32.086221 38.180329 239 0 0 32.02988 38.164761 240 0 0 32.146192 38.226919 241 0 0 31.962017 38.088003 242 0 0 32.038671 38.146619 243 0 0 32.076745 38.184463 244 0 0 31.955435 38.112453 245 0 0 31.985791 38.131719 246 0 0 31.946108 38.105964 247 0 0 31.808592 38.004492 248 0 0 31.720452 37.934205 249 0 0 31.781419 37.972359 250 0 0 31.728372 37.979983 251 0 0 31.710467 37.943867 252 0 0 31.660758 37.911682 253 0 0 31.671273 37.921227 254 0 0 31.613866 37.915442 255 0 0 31.519511 37.82822 256 0 0 31.763154 38.005164 257 0 0 31.52502 37.816732 258 0 0 31.451676 37.790405 259 0 0 31.317272 37.681449 260 0 0 31.218079 37.641634 261 0 0 31.254013 37.654201 262 0 0 31.154013 37.612913 263 0 0 31.494694 37.80525 264 0 0 31.038454 37.527199 265 0 0 31.207188 37.633805 266 0 0 31.03899 37.506532 267 0 0 31.081434 37.553184 268 0 0 30.978104 37.496528 269 0 0 30.884724 37.458415 270 0 0 30.89013 37.475361 271 0 0 30.9766 37.489103 272 0 0 30.75282 37.357065 273 0 0 30.812816 37.407854 274 0 0 30.735026 37.327664 275 0 0 30.750442 37.364065 276 0 0 30.516271 37.202996 277 0 0 30.342451 37.074785 278 0 0 30.457919 37.171283 279 0 0 30.357712 37.069746 280 0 0 30.180692 36.996716 281 0 0 29.95544 36.761767 282 0 0 30.077198 36.948435 283 0 0 29.971957 36.822291 284 0 0 29.597072 36.591449 285 0 0 29.51774 36.546102 286 0 0 29.702869 36.618966 287 0 0 29.958333 36.794256 288 0 0 29.598532 36.593394 289 0 0 29.369237 36.432099 290 0 0 29.255477 36.343505 291 0 0 29.694094 36.60353 292 0 0 29.473328 36.471493 293 0 0 29.215453 36.368065 294 0 0 29.275973 36.331808 295 0 0 29.283532 36.406364 296 0 0 29.141713 36.277082 297 0 0 28.923879 36.106361 298 0 0 29.14278 36.259501 299 0 0 28.998275 36.170979 300 0 0 29.104844 36.19579 301 0 0 29.159923 36.277243 302 0 0 28.911685 36.016304 303 0 0 28.831782 35.946791 304 0 0 28.706415 35.894591 305 0 0 28.368337 35.716521 306 0 0 28.309824 35.580744 307 0 0 28.10583 35.530942 308 0 0 28.717181 35.884492 309 0 0 28.30896 35.678338 310 0 0 28.102397 35.568627 311 0 0 29.144009 36.242704 312 0 0 28.015892 35.603097 313 0 0 27.897368 35.281579 314 0 0 27.856742 35.351124 315 0 0 27.667683 35.363821 316 0 0 28.315359 35.698802 317 0 0 27.789007 35.406619 318 0 0 28.497121 35.891875 319 0 0 28.240166 35.461698 320 0 0 27.622222 35.220741 321 0 0 27.294686 34.830918 322 0 0 27.784 35.216889 323 0 0 28.005882 35.396078 324 0 0 27.633441 35.163987 325 0 0 27.711191 35.34657 326 0 0 28.241803 35.627049 327 0 0 27.848889 35.308148 328 0 0 28.546341 35.656911 329 0 0 27.471204 34.970332 330 0 0 28.325444 35.854043 331 0 0 27.364238 35.154525 332 0 0 27.929078 35.41844 333 0 0 26.753968 34.867725 334 0 0 27.027027 35.144144 335 0 0 27.303371 34.865169 336 0 0 27.794872 35.213675 337 0 0 28.323529 35.480392 338 0 0 26.068966 34.632184 339 0 0 27.588235 34.960784 340 0 0 25.130435 33.108696 341 0 0 27.512821 35.179487 342 0 0 29.685714 35.780952 343 0 0 30.62069 37.183908 344 0 0 29.44 35.826667 345 0 0 26 34.333333 346 0 0 27.947368 35.666667 347 0 0 29.8125 36.708333 348 0 0 28.214286 34.738095 349 0 0 31.727273 38.363636 350 0 0 32.3 38.166667 351 0 0 30.444444 37.333333 352 0 0 25.428571 33.47619 353 0 0 22.333333 32.722222 354 0 0 31 37.944444 355 0 0 27.4 35.333333 356 0 0 32.666667 38.111111 357 0 0 18.333333 28.888889 358 0 0 25.333333 33 359 0 0 25.333333 34 360 0 0 27.333333 32.444444 361 0 0 31.333333 38.555556 362 0 0 32 37.777778 363 0 0 36 41 364 0 0 27 33.166667 365 0 0 36 41 366 0 0 26.5 37 367 0 0 29.5 38 368 0 0 36 41 369 0 0 31 37.833333 370 0 0 33.5 38.833333 371 0 0 34 39.833333 372 0 0 31 38.5