## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5386-Z0071-CGTGCGCAAGCAGAT/441525-L5386-Z0071-CGTGCGCAAGCAGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5386-Z0071-CGTGCGCAAGCAGAT/441525-L5386-Z0071-CGTGCGCAAGCAGAT_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 03:00:03 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 998503 998503 144 144168845 144168845 139296749 139296749 130053007 130053007 0 0 0.966206 0.902088 0 0.966206 0.902088 0 432506535 432506535 426094581 426094581 411306101 411306101 386080401 386080401 0.985175 0.950982 0.892658 0.985175 0.950982 0.892658 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 935 0 35.992681 40.994411 1 11834 0 35.985906 40.990199 2 14235 4820 35.993817 40.994887 3 35718 1393 35.982788 40.986212 4 57950 50254 35.991445 40.993118 5 115285 17311 35.995343 40.996096 6 109496 130325 35.981633 40.985698 7 200347 162839 35.985733 40.990201 8 190622 151490 35.990614 40.992241 9 239537 111384 35.96258 40.968903 10 249193 514152 35.877131 40.928078 11 294885 63810 35.909214 40.931989 12 347367 709960 35.345703 40.449655 13 345105 198053 34.075513 39.8083 14 456857 981035 35.881489 40.927827 15 373295 370971 35.802365 40.85981 16 380421 424147 35.775184 40.800059 17 517016 1092861 35.894441 40.911574 18 550958 726948 35.716336 40.765309 19 381040 700201 35.718799 40.791777 20 520981 987603 35.897897 40.933063 21 664639 1385213 35.834722 40.880497 22 334728 552547 35.611935 40.736536 23 1052081 1244907 35.356442 40.566724 24 590625 1218054 35.346669 40.559782 25 546098 490692 35.334117 40.54956 26 1755090 2522086 35.28594 40.514364 27 367998 906222 35.30554 40.529666 28 964127 406779 35.318336 40.539484 29 2447375 5074377 35.318208 40.53783 30 795548 42318 35.309708 40.531727 31 2387275 883125 35.307797 40.528388 32 1708410 5417702 35.303206 40.52468 33 871067 130865 35.294152 40.519009 34 2525845 2832461 35.293413 40.518192 35 2301062 3834881 35.305783 40.527233 36 119463800 2238461 35.328616 40.54265 37 0 4272799 35.331671 40.545968 38 0 436640 35.321482 40.539933 39 0 5136448 35.314462 40.533239 40 0 0 35.311247 40.530613 41 0 386080401 35.296262 40.519766 42 0 0 35.288966 40.514641 43 0 0 35.2964 40.520306 44 0 0 35.303756 40.524438 45 0 0 35.303459 40.523874 46 0 0 35.298233 40.520032 47 0 0 35.295697 40.519119 48 0 0 35.280849 40.508523 49 0 0 35.276657 40.505888 50 0 0 35.275842 40.504387 51 0 0 35.26906 40.500261 52 0 0 35.260486 40.494698 53 0 0 35.258905 40.49307 54 0 0 35.24845 40.48651 55 0 0 35.239424 40.480308 56 0 0 35.217632 40.46587 57 0 0 35.21765 40.464743 58 0 0 35.205023 40.454289 59 0 0 35.18757 40.44146 60 0 0 35.153741 40.417843 61 0 0 35.127143 40.39772 62 0 0 35.094229 40.374566 63 0 0 35.060734 40.348784 64 0 0 35.031484 40.325552 65 0 0 34.989331 40.294734 66 0 0 34.938029 40.258603 67 0 0 34.889193 40.222972 68 0 0 34.833024 40.179862 69 0 0 34.771247 40.133509 70 0 0 34.706543 40.083719 71 0 0 34.635353 40.026427 72 0 0 34.566399 39.970916 73 0 0 34.476397 39.898725 74 0 0 34.396217 39.835582 75 0 0 34.326541 39.781573 76 0 0 34.234161 39.710694 77 0 0 34.149988 39.644343 78 0 0 34.075169 39.591121 79 0 0 33.987999 39.522226 80 0 0 33.920716 39.465961 81 0 0 33.861453 39.418928 82 0 0 33.792135 39.363333 83 0 0 33.730502 39.314249 84 0 0 33.697811 39.284627 85 0 0 33.651782 39.24792 86 0 0 33.602325 39.208022 87 0 0 33.570881 39.183376 88 0 0 33.53034 39.145061 89 0 0 33.476164 39.100618 90 0 0 33.431121 39.062543 91 0 0 33.395295 39.031141 92 0 0 33.357933 38.997722 93 0 0 33.323314 38.967976 94 0 0 33.298813 38.945077 95 0 0 33.258277 38.913263 96 0 0 33.241336 38.895487 97 0 0 33.217583 38.877976 98 0 0 33.223609 38.883524 99 0 0 33.22092 38.879831 100 0 0 33.240503 38.895692 101 0 0 33.26621 38.914913 102 0 0 33.302671 38.941269 103 0 0 33.331806 38.962351 104 0 0 33.34984 38.974149 105 0 0 33.368609 38.986401 106 0 0 33.378627 38.992986 107 0 0 33.390478 38.999218 108 0 0 33.386811 38.99501 109 0 0 33.386195 38.997297 110 0 0 33.345352 38.964843 111 0 0 33.314368 38.940572 112 0 0 33.282193 38.912035 113 0 0 33.21308 38.853764 114 0 0 33.169462 38.815901 115 0 0 33.132784 38.786455 116 0 0 33.085945 38.750391 117 0 0 33.061003 38.732919 118 0 0 33.049099 38.729421 119 0 0 33.04272 38.726389 120 0 0 33.055184 38.738158 121 0 0 33.074866 38.750338 122 0 0 33.077071 38.749805 123 0 0 33.08797 38.758343 124 0 0 33.102584 38.769879 125 0 0 33.127974 38.781994 126 0 0 33.138296 38.788064 127 0 0 33.147401 38.790945 128 0 0 33.135794 38.777955 129 0 0 33.120197 38.761863 130 0 0 33.105144 38.75196 131 0 0 33.082266 38.734264 132 0 0 33.076341 38.728299 133 0 0 33.067607 38.721483 134 0 0 33.060697 38.713076 135 0 0 33.058516 38.70725 136 0 0 33.036576 38.691217 137 0 0 33.033524 38.689539 138 0 0 33.017354 38.675483 139 0 0 33.033074 38.692677 140 0 0 33.060071 38.716722 141 0 0 33.08106 38.733039 142 0 0 33.111108 38.758554 143 0 0 33.122504 38.765645 144 0 0 33.107919 38.751639 145 0 0 33.091847 38.736219 146 0 0 33.081236 38.725118 147 0 0 33.040975 38.685264 148 0 0 33.017069 38.666166 149 0 0 32.97576 38.630242 150 0 0 32.92312 38.587766 151 0 0 32.898355 38.570381 152 0 0 32.882211 38.560552 153 0 0 32.859438 38.544426 154 0 0 32.862956 38.543343 155 0 0 32.866421 38.547702 156 0 0 32.858218 38.535979 157 0 0 32.878679 38.551584 158 0 0 32.906159 38.574262 159 0 0 32.922615 38.586276 160 0 0 32.947688 38.605079 161 0 0 32.981992 38.63082 162 0 0 33.005821 38.652562 163 0 0 33.019157 38.661636 164 0 0 33.036151 38.674003 165 0 0 33.019569 38.663749 166 0 0 33.000115 38.640321 167 0 0 32.940506 38.58865 168 0 0 32.920468 38.566941 169 0 0 32.857131 38.513503 170 0 0 32.799383 38.461286 171 0 0 32.765277 38.434472 172 0 0 32.754161 38.428464 173 0 0 32.710646 38.394799 174 0 0 32.73205 38.411172 175 0 0 32.742069 38.424556 176 0 0 32.757017 38.433365 177 0 0 32.801699 38.470396 178 0 0 32.817762 38.483758 179 0 0 32.85741 38.517739 180 0 0 32.891229 38.546794 181 0 0 32.937383 38.585198 182 0 0 33.011196 38.646655 183 0 0 33.078611 38.69522 184 0 0 33.117363 38.7311 185 0 0 33.135477 38.74826 186 0 0 33.187452 38.78751 187 0 0 33.216313 38.81302 188 0 0 33.241758 38.83087 189 0 0 33.223301 38.820206 190 0 0 33.245767 38.834808 191 0 0 33.206312 38.812728 192 0 0 33.166291 38.783411 193 0 0 33.139405 38.77208 194 0 0 33.125234 38.768004 195 0 0 33.137248 38.773007 196 0 0 33.12109 38.768573 197 0 0 33.10583 38.764242 198 0 0 33.087326 38.755675 199 0 0 33.088699 38.762501 200 0 0 33.055122 38.744635 201 0 0 33.076158 38.774064 202 0 0 33.035847 38.750181 203 0 0 32.989911 38.715846 204 0 0 32.987188 38.724583 205 0 0 32.94962 38.700388 206 0 0 32.928794 38.695723 207 0 0 32.929493 38.702308 208 0 0 32.929986 38.697383 209 0 0 32.872491 38.66714 210 0 0 32.864559 38.667159 211 0 0 32.833724 38.64541 212 0 0 32.840928 38.660971 213 0 0 32.805279 38.636403 214 0 0 32.813352 38.646533 215 0 0 32.79344 38.634088 216 0 0 32.743404 38.59762 217 0 0 32.727392 38.583737 218 0 0 32.721636 38.586076 219 0 0 32.712949 38.57404 220 0 0 32.704257 38.58351 221 0 0 32.669899 38.554215 222 0 0 32.649015 38.531313 223 0 0 32.615936 38.524461 224 0 0 32.645727 38.54503 225 0 0 32.605636 38.524576 226 0 0 32.57148 38.50275 227 0 0 32.569819 38.486367 228 0 0 32.562357 38.488406 229 0 0 32.499861 38.447987 230 0 0 32.436734 38.410706 231 0 0 32.425588 38.4041 232 0 0 32.412521 38.413983 233 0 0 32.430968 38.415595 234 0 0 32.349861 38.363749 235 0 0 32.363983 38.369765 236 0 0 32.312332 38.340996 237 0 0 32.380701 38.389585 238 0 0 32.318592 38.359936 239 0 0 32.254027 38.314669 240 0 0 32.26924 38.304657 241 0 0 32.242861 38.29659 242 0 0 32.169435 38.235425 243 0 0 32.199072 38.257427 244 0 0 32.146097 38.231524 245 0 0 32.114579 38.210922 246 0 0 32.117774 38.232993 247 0 0 32.131418 38.244644 248 0 0 32.066392 38.187947 249 0 0 32.021333 38.168147 250 0 0 31.952148 38.126377 251 0 0 31.901925 38.077612 252 0 0 31.927622 38.102148 253 0 0 31.926646 38.104182 254 0 0 31.881163 38.066049 255 0 0 31.886778 38.074771 256 0 0 31.865148 38.075155 257 0 0 31.774247 38.049755 258 0 0 31.778548 38.002995 259 0 0 31.79707 38.036786 260 0 0 31.709334 37.973659 261 0 0 31.641311 37.941485 262 0 0 31.619781 37.902755 263 0 0 31.580349 37.901854 264 0 0 31.5799 37.906672 265 0 0 31.365541 37.756648 266 0 0 31.434328 37.796488 267 0 0 31.398633 37.772171 268 0 0 31.312287 37.714259 269 0 0 31.158347 37.626121 270 0 0 31.133835 37.594446 271 0 0 31.177719 37.675021 272 0 0 31.091836 37.587311 273 0 0 30.983736 37.519952 274 0 0 30.907979 37.478444 275 0 0 30.951663 37.510532 276 0 0 30.933752 37.475676 277 0 0 30.778677 37.402647 278 0 0 30.716567 37.327014 279 0 0 30.576425 37.242463 280 0 0 30.377524 37.06262 281 0 0 30.580025 37.243382 282 0 0 30.333667 37.057884 283 0 0 30.372486 37.104564 284 0 0 30.181234 36.987507 285 0 0 30.12351 36.939004 286 0 0 30.061138 36.849349 287 0 0 29.973832 36.844635 288 0 0 29.853422 36.743067 289 0 0 29.857588 36.72176 290 0 0 29.809977 36.730468 291 0 0 29.84244 36.747035 292 0 0 29.56743 36.534043 293 0 0 29.5846 36.550602 294 0 0 29.468412 36.517743 295 0 0 29.365805 36.405627 296 0 0 29.376956 36.443774 297 0 0 29.211576 36.323035 298 0 0 29.076626 36.20664 299 0 0 29.148999 36.289779 300 0 0 28.848191 36.089291 301 0 0 28.995823 36.186354 302 0 0 29.007554 36.172027 303 0 0 28.980061 36.197001 304 0 0 28.942641 36.083604 305 0 0 28.816514 36.023222 306 0 0 28.67561 35.92185 307 0 0 28.528877 35.782392 308 0 0 28.777011 35.98205 309 0 0 28.714233 35.969229 310 0 0 28.862637 36.069466 311 0 0 28.547059 35.77563 312 0 0 28.509698 35.832356 313 0 0 28.684414 35.853662 314 0 0 28.610592 35.905677 315 0 0 28.463606 35.717059 316 0 0 28.105549 35.520306 317 0 0 28.339181 35.641109 318 0 0 28.278336 35.725968 319 0 0 28.182889 35.4236 320 0 0 27.98532 35.435809 321 0 0 28.1238 35.442099 322 0 0 28.269926 35.448105 323 0 0 28.569606 35.96249 324 0 0 28.157161 35.60583 325 0 0 28.166193 35.576705 326 0 0 27.858521 35.167203 327 0 0 28.287744 35.650681 328 0 0 27.741551 35.373095 329 0 0 28.401316 35.648392 330 0 0 27.796117 34.979773 331 0 0 26.949868 34.790677 332 0 0 27.366569 34.923754 333 0 0 28.47 35.737778 334 0 0 28.325758 35.454545 335 0 0 27.451327 34.713864 336 0 0 27.928571 35.323129 337 0 0 27.143713 34.818363 338 0 0 28.092715 35.136865 339 0 0 27.933333 35.597531 340 0 0 29.330508 36.237288 341 0 0 27.183486 35.079511 342 0 0 27.989691 34.879725 343 0 0 28.05618 34.88015 344 0 0 28.891892 36.405405 345 0 0 27.357143 35.004762 346 0 0 27.711864 35.367232 347 0 0 25.928571 34.083333 348 0 0 27.75 35.448718 349 0 0 26.604167 34.069444 350 0 0 24.975 34.166667 351 0 0 25.864865 33.792793 352 0 0 28.125 35.5 353 0 0 26.541667 35.166667 354 0 0 26.130435 34.623188 355 0 0 30.4 37.05 356 0 0 24.2 31.8 357 0 0 28.5 35.761905 358 0 0 29.538462 37 359 0 0 28.666667 36.740741 360 0 0 30.75 37.5 361 0 0 34.5 39.875 362 0 0 33.125 38.875 363 0 0 23.833333 31.222222 364 0 0 31 37.666667 365 0 0 26 33.555556 366 0 0 23.333333 31.611111 367 0 0 31.2 36.6 368 0 0 33.6 39.533333 369 0 0 34.6 40.2 370 0 0 32.25 38.333333 371 0 0 31 37.416667 372 0 0 30.5 37.333333 373 0 0 23.5 35.166667 374 0 0 13.5 22.666667 375 0 0 19.5 27.166667 376 0 0 29.5 38 377 0 0 20 29