## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5392-Z0078-CAGCCGCTGCTCGAT/441525-L5392-Z0078-CAGCCGCTGCTCGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5392-Z0078-CAGCCGCTGCTCGAT/441525-L5392-Z0078-CAGCCGCTGCTCGAT_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 998385 998385 140 140143440 140143440 135130985 135130985 125734138 125734138 0 0 0.964233 0.897182 0 0.964233 0.897182 0 420430320 420430320 413824730 413824730 398717428 398717428 373248064 373248064 0.984289 0.948356 0.887776 0.984289 0.948356 0.887776 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 948 0 35.993848 40.995271 1 12032 0 35.984622 40.989566 2 14932 4970 35.993137 40.994091 3 36685 1350 35.981012 40.984615 4 58834 52055 35.98713 40.989812 5 119410 18422 35.993034 40.994206 6 111816 135186 35.972328 40.976759 7 207044 168801 35.971296 40.980912 8 197776 156061 35.98506 40.987672 9 248040 116531 35.951377 40.958853 10 260192 524315 35.88683 40.93071 11 303820 66984 35.921566 40.941701 12 359993 730244 35.22809 40.355054 13 356328 204999 33.787833 39.63217 14 470150 1009829 35.877857 40.924698 15 384295 382807 35.841947 40.8881 16 389213 437973 35.81735 40.839645 17 530210 1119469 35.909421 40.925374 18 563122 755983 35.709834 40.760895 19 387615 719611 35.721977 40.794926 20 530546 1008284 35.895721 40.930654 21 687259 1432609 35.815466 40.865332 22 338703 565513 35.579979 40.712219 23 1073133 1271496 35.265652 40.488599 24 605190 1255211 35.289895 40.515941 25 558012 494144 35.293341 40.520413 26 1770635 2568373 35.219053 40.458794 27 378653 924157 35.251209 40.490504 28 982004 419940 35.259359 40.498375 29 2472712 5167575 35.248622 40.487936 30 804503 42191 35.258319 40.494868 31 2408454 885148 35.249174 40.487031 32 1721268 5524122 35.233743 40.472894 33 879714 133566 35.243565 40.482661 34 2535454 2875070 35.242601 40.482614 35 2281337 3881383 35.260642 40.495686 36 115103408 2278142 35.292643 40.516231 37 0 4296747 35.283668 40.512137 38 0 408699 35.27604 40.507175 39 0 5144296 35.274198 40.506462 40 0 0 35.263029 40.497845 41 0 373248064 35.254293 40.491221 42 0 0 35.244507 40.484576 43 0 0 35.251833 40.488554 44 0 0 35.25856 40.492545 45 0 0 35.265248 40.497734 46 0 0 35.254548 40.490032 47 0 0 35.252041 40.486148 48 0 0 35.229193 40.471774 49 0 0 35.226094 40.470329 50 0 0 35.223865 40.468021 51 0 0 35.228519 40.47088 52 0 0 35.191473 40.445622 53 0 0 35.184667 40.446414 54 0 0 35.190546 40.44838 55 0 0 35.176683 40.438434 56 0 0 35.149776 40.425331 57 0 0 35.163829 40.427547 58 0 0 35.155199 40.420368 59 0 0 35.127708 40.399842 60 0 0 35.109745 40.384748 61 0 0 35.078087 40.362502 62 0 0 35.036022 40.330931 63 0 0 35.007309 40.309038 64 0 0 34.973545 40.282393 65 0 0 34.926268 40.250146 66 0 0 34.875181 40.212784 67 0 0 34.827125 40.176693 68 0 0 34.76229 40.128287 69 0 0 34.700525 40.080902 70 0 0 34.632397 40.028999 71 0 0 34.56091 39.970579 72 0 0 34.476829 39.905645 73 0 0 34.393551 39.83789 74 0 0 34.306957 39.769132 75 0 0 34.224128 39.705038 76 0 0 34.139385 39.639121 77 0 0 34.053373 39.573087 78 0 0 33.968433 39.507115 79 0 0 33.886161 39.441177 80 0 0 33.797479 39.373715 81 0 0 33.728636 39.314658 82 0 0 33.655801 39.255833 83 0 0 33.583884 39.197091 84 0 0 33.525871 39.150257 85 0 0 33.484013 39.117774 86 0 0 33.417046 39.063833 87 0 0 33.385611 39.038865 88 0 0 33.320793 38.984255 89 0 0 33.275378 38.94515 90 0 0 33.227284 38.903862 91 0 0 33.18042 38.863274 92 0 0 33.130235 38.81889 93 0 0 33.099059 38.793955 94 0 0 33.061698 38.759751 95 0 0 33.041741 38.740832 96 0 0 33.0137 38.719404 97 0 0 32.996663 38.705108 98 0 0 32.980658 38.690808 99 0 0 32.995427 38.704465 100 0 0 33.011919 38.714166 101 0 0 33.041035 38.736686 102 0 0 33.067202 38.754128 103 0 0 33.079148 38.762905 104 0 0 33.106097 38.783312 105 0 0 33.12034 38.79155 106 0 0 33.113007 38.782704 107 0 0 33.118509 38.784221 108 0 0 33.108882 38.776613 109 0 0 33.096794 38.77065 110 0 0 33.088696 38.763502 111 0 0 33.048529 38.726894 112 0 0 32.993744 38.684386 113 0 0 32.940052 38.638592 114 0 0 32.876081 38.587205 115 0 0 32.828271 38.547335 116 0 0 32.78237 38.511273 117 0 0 32.755883 38.493412 118 0 0 32.751993 38.495376 119 0 0 32.758833 38.501731 120 0 0 32.763649 38.506731 121 0 0 32.767639 38.505544 122 0 0 32.771138 38.50959 123 0 0 32.774233 38.510756 124 0 0 32.799019 38.528185 125 0 0 32.823309 38.543872 126 0 0 32.830938 38.543957 127 0 0 32.849057 38.556191 128 0 0 32.832908 38.540222 129 0 0 32.823572 38.530515 130 0 0 32.803972 38.515791 131 0 0 32.783253 38.4984 132 0 0 32.775546 38.490324 133 0 0 32.772276 38.484365 134 0 0 32.764631 38.478036 135 0 0 32.766246 38.474377 136 0 0 32.748245 38.460314 137 0 0 32.745419 38.459628 138 0 0 32.74639 38.461384 139 0 0 32.768902 38.482966 140 0 0 32.803438 38.511284 141 0 0 32.814362 38.522357 142 0 0 32.848467 38.547273 143 0 0 32.836643 38.536509 144 0 0 32.846226 38.540259 145 0 0 32.843193 38.536935 146 0 0 32.810691 38.508967 147 0 0 32.766269 38.470301 148 0 0 32.75472 38.45828 149 0 0 32.730863 38.437913 150 0 0 32.677597 38.394044 151 0 0 32.664214 38.38755 152 0 0 32.638437 38.366747 153 0 0 32.632736 38.363868 154 0 0 32.620067 38.348125 155 0 0 32.603735 38.329724 156 0 0 32.641776 38.366606 157 0 0 32.652815 38.373631 158 0 0 32.669714 38.389331 159 0 0 32.707158 38.417553 160 0 0 32.7291 38.435473 161 0 0 32.776176 38.467701 162 0 0 32.820702 38.505126 163 0 0 32.833236 38.516807 164 0 0 32.860924 38.534314 165 0 0 32.861891 38.536812 166 0 0 32.834762 38.51431 167 0 0 32.80473 38.482584 168 0 0 32.77004 38.448621 169 0 0 32.716754 38.407563 170 0 0 32.664141 38.36012 171 0 0 32.660452 38.355248 172 0 0 32.628528 38.326348 173 0 0 32.625897 38.332843 174 0 0 32.629084 38.337315 175 0 0 32.644918 38.350326 176 0 0 32.667203 38.372943 177 0 0 32.694099 38.391778 178 0 0 32.746436 38.432906 179 0 0 32.779404 38.460334 180 0 0 32.822963 38.499755 181 0 0 32.883035 38.552299 182 0 0 32.927991 38.58538 183 0 0 32.969444 38.62209 184 0 0 33.053103 38.688617 185 0 0 33.047272 38.686673 186 0 0 33.091257 38.719919 187 0 0 33.098419 38.726874 188 0 0 33.131568 38.751993 189 0 0 33.141266 38.758294 190 0 0 33.12506 38.754678 191 0 0 33.106908 38.740692 192 0 0 33.119347 38.75753 193 0 0 33.056505 38.708298 194 0 0 33.021064 38.693122 195 0 0 33.018265 38.694344 196 0 0 33.008772 38.688028 197 0 0 33.005769 38.690045 198 0 0 32.990115 38.681356 199 0 0 32.986583 38.697485 200 0 0 32.983976 38.697166 201 0 0 32.972845 38.705407 202 0 0 32.929448 38.678827 203 0 0 32.888797 38.652879 204 0 0 32.902473 38.668584 205 0 0 32.86873 38.645792 206 0 0 32.831821 38.634335 207 0 0 32.827268 38.629859 208 0 0 32.828583 38.62813 209 0 0 32.839251 38.647028 210 0 0 32.769829 38.590023 211 0 0 32.743153 38.580707 212 0 0 32.723813 38.56935 213 0 0 32.703197 38.557413 214 0 0 32.669812 38.542125 215 0 0 32.666045 38.537533 216 0 0 32.624058 38.511056 217 0 0 32.65292 38.527719 218 0 0 32.605549 38.497256 219 0 0 32.569928 38.470406 220 0 0 32.547536 38.470976 221 0 0 32.579002 38.48623 222 0 0 32.462486 38.411242 223 0 0 32.466099 38.422063 224 0 0 32.466175 38.421545 225 0 0 32.466652 38.41864 226 0 0 32.448947 38.40444 227 0 0 32.389395 38.371271 228 0 0 32.402989 38.383997 229 0 0 32.358646 38.339429 230 0 0 32.378681 38.374382 231 0 0 32.26802 38.306846 232 0 0 32.309711 38.335941 233 0 0 32.312512 38.32559 234 0 0 32.259949 38.291766 235 0 0 32.213735 38.256119 236 0 0 32.199633 38.243038 237 0 0 32.250768 38.28576 238 0 0 32.213743 38.270105 239 0 0 32.141184 38.207614 240 0 0 32.117248 38.201001 241 0 0 32.079143 38.169231 242 0 0 31.976698 38.128829 243 0 0 32.033647 38.164936 244 0 0 31.958282 38.120451 245 0 0 31.941146 38.085705 246 0 0 31.98331 38.119611 247 0 0 31.889384 38.049295 248 0 0 31.898312 38.085087 249 0 0 31.839909 38.044335 250 0 0 31.714833 37.963022 251 0 0 31.780578 38.012539 252 0 0 31.684222 37.961153 253 0 0 31.57835 37.869701 254 0 0 31.662092 37.926567 255 0 0 31.505715 37.807499 256 0 0 31.562246 37.853997 257 0 0 31.456824 37.775488 258 0 0 31.536155 37.856191 259 0 0 31.449884 37.800742 260 0 0 31.462982 37.817945 261 0 0 31.221972 37.633539 262 0 0 31.346642 37.724272 263 0 0 31.135818 37.579779 264 0 0 31.199595 37.622359 265 0 0 31.123796 37.587383 266 0 0 31.001685 37.514923 267 0 0 31.014841 37.482436 268 0 0 31.046905 37.540643 269 0 0 31.021663 37.532051 270 0 0 30.847531 37.417734 271 0 0 30.810667 37.346413 272 0 0 30.828423 37.411811 273 0 0 30.658689 37.304304 274 0 0 30.615259 37.311451 275 0 0 30.507335 37.165293 276 0 0 30.531751 37.18955 277 0 0 30.420898 37.097055 278 0 0 30.274404 36.994802 279 0 0 30.182919 36.932843 280 0 0 30.161189 36.96142 281 0 0 30.041963 36.854046 282 0 0 29.942279 36.806823 283 0 0 30.176511 36.940082 284 0 0 29.736128 36.667489 285 0 0 29.945808 36.858762 286 0 0 29.790781 36.655691 287 0 0 29.561047 36.525517 288 0 0 29.739948 36.659799 289 0 0 29.608561 36.570099 290 0 0 29.494531 36.528344 291 0 0 29.535977 36.508577 292 0 0 29.417727 36.393505 293 0 0 29.23201 36.33558 294 0 0 28.916208 36.071202 295 0 0 29.28292 36.306302 296 0 0 29.269293 36.319112 297 0 0 29.200508 36.335401 298 0 0 29.092267 36.188049 299 0 0 28.676026 35.889335 300 0 0 28.775292 35.98984 301 0 0 28.812967 36.077619 302 0 0 28.57418 35.844151 303 0 0 28.502806 35.781145 304 0 0 28.931319 36.110413 305 0 0 28.193158 35.610207 306 0 0 28.569217 35.803922 307 0 0 28.321931 35.752734 308 0 0 28.3857 35.7286 309 0 0 28.447777 35.726477 310 0 0 28.082427 35.452967 311 0 0 28.126004 35.526868 312 0 0 28.252 35.641556 313 0 0 27.731354 35.168236 314 0 0 27.791373 35.393203 315 0 0 28.166949 35.525141 316 0 0 27.514339 35.021277 317 0 0 28.04467 35.320812 318 0 0 27.570634 35.073044 319 0 0 27.900978 35.476365 320 0 0 28.290366 35.531434 321 0 0 27.843844 35.348348 322 0 0 28.616949 35.901695 323 0 0 27.932961 35.405338 324 0 0 27.578629 35.005376 325 0 0 27.377273 34.99697 326 0 0 27.895262 35.517872 327 0 0 27.471074 34.906336 328 0 0 27.679012 35.19856 329 0 0 28.074468 35.489362 330 0 0 27.78629 35.40457 331 0 0 28.12963 35.450617 332 0 0 27.727749 35.338569 333 0 0 28.482558 35.736434 334 0 0 27.398693 34.816993 335 0 0 27.078014 34.680851 336 0 0 28.451128 35.829574 337 0 0 27.872881 35.463277 338 0 0 27.2 35.247619 339 0 0 26.384615 34.278388 340 0 0 29.084337 36.301205 341 0 0 29 35.890476 342 0 0 28.852459 36.169399 343 0 0 28.127273 35.515152 344 0 0 25.847826 34.463768 345 0 0 29.837838 37.216216 346 0 0 25.875 33.979167 347 0 0 25.925926 33.234568 348 0 0 25.875 33.333333 349 0 0 26.571429 35.063492 350 0 0 26.6875 34.541667 351 0 0 23.333333 31.888889 352 0 0 26.571429 33.404762 353 0 0 29.214286 36.119048 354 0 0 27.846154 35.410256 355 0 0 27.875 34.541667 356 0 0 19.5 27.055556 357 0 0 28.333333 36.611111 358 0 0 33.6 39.466667 359 0 0 25.6 31.933333 360 0 0 27.2 35.466667 361 0 0 35 40.2 362 0 0 25.6 34.2 363 0 0 17.333333 28.666667 364 0 0 15 25.888889 365 0 0 27.666667 36.111111 366 0 0 20 26.777778 367 0 0 21.333333 28.555556 368 0 0 26 35.333333 369 0 0 14 21.333333 370 0 0 35 39.666667 371 0 0 36 41 372 0 0 35 39.666667