## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5268-Z0005-CATGTATCCTCTGAT/441525-L5268-Z0005-CATGTATCCTCTGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5268-Z0005-CATGTATCCTCTGAT/441525-L5268-Z0005-CATGTATCCTCTGAT_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 03:02:07 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 998880 998880 142 142119375 142119375 137005567 137005567 127375327 127375327 0 0 0.964018 0.896256 0 0.964018 0.896256 0 426358125 426358125 419626551 419626551 404193575 404193575 378325585 378325585 0.984211 0.948014 0.887342 0.984211 0.948014 0.887342 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 996 0 35.995354 40.996578 1 12752 0 35.988514 40.992292 2 15195 5195 35.992361 40.99351 3 38358 1451 35.977872 40.982161 4 59883 53984 35.98881 40.991111 5 120107 18529 35.992548 40.99432 6 112767 138740 35.972243 40.977518 7 210164 173049 35.97879 40.985416 8 197198 154829 35.9862 40.989172 9 252872 119099 35.948594 40.957263 10 264771 525142 35.893259 40.92951 11 312292 67742 35.939477 40.956451 12 367689 739100 35.321511 40.429847 13 364874 217181 33.993699 39.755589 14 481459 1033851 35.895275 40.935973 15 391619 393968 35.826779 40.878982 16 398562 444233 35.800046 40.824617 17 540776 1144815 35.906786 40.921857 18 580204 767630 35.697598 40.751565 19 391270 733036 35.768146 40.82597 20 548947 1032982 35.918114 40.944967 21 699139 1451882 35.831263 40.878583 22 349757 579108 35.584379 40.717993 23 1116874 1316684 35.26145 40.500555 24 613849 1276299 35.281609 40.514469 25 558577 506561 35.270488 40.506716 26 1846511 2656621 35.216208 40.463013 27 386334 945139 35.253534 40.494967 28 982263 415276 35.260409 40.500856 29 2527989 5252424 35.251339 40.492885 30 812152 42259 35.247619 40.488618 31 2443891 906713 35.244835 40.484963 32 1724360 5571842 35.232764 40.475473 33 897665 134150 35.245345 40.484932 34 2592554 2855205 35.227093 40.473426 35 2335453 3971992 35.249341 40.488725 36 116569252 2297292 35.272275 40.504832 37 0 4414242 35.274857 40.508946 38 0 417189 35.260057 40.498248 39 0 5257106 35.26084 40.498798 40 0 1 35.253264 40.491903 41 0 378325584 35.240283 40.483959 42 0 0 35.233057 40.477198 43 0 0 35.242442 40.484198 44 0 0 35.246167 40.48775 45 0 0 35.249201 40.487634 46 0 0 35.240647 40.482381 47 0 0 35.234166 40.478111 48 0 0 35.225175 40.47214 49 0 0 35.219845 40.468589 50 0 0 35.222601 40.469755 51 0 0 35.211929 40.462321 52 0 0 35.202671 40.456294 53 0 0 35.190066 40.450829 54 0 0 35.186168 40.446193 55 0 0 35.177236 40.438989 56 0 0 35.15229 40.424944 57 0 0 35.155684 40.422971 58 0 0 35.128061 40.404084 59 0 0 35.100189 40.382294 60 0 0 35.065198 40.355822 61 0 0 35.021264 40.321327 62 0 0 34.973926 40.286646 63 0 0 34.92285 40.249006 64 0 0 34.863365 40.201785 65 0 0 34.789251 40.147098 66 0 0 34.728758 40.101045 67 0 0 34.642063 40.036197 68 0 0 34.570111 39.980814 69 0 0 34.485553 39.915101 70 0 0 34.388452 39.840036 71 0 0 34.300221 39.772228 72 0 0 34.202045 39.691606 73 0 0 34.116889 39.623998 74 0 0 34.030618 39.555298 75 0 0 33.948258 39.488532 76 0 0 33.863093 39.423521 77 0 0 33.80238 39.37744 78 0 0 33.726613 39.318962 79 0 0 33.680272 39.28291 80 0 0 33.619162 39.232906 81 0 0 33.577777 39.20075 82 0 0 33.540909 39.166708 83 0 0 33.489653 39.124474 84 0 0 33.467257 39.106168 85 0 0 33.432677 39.075452 86 0 0 33.405138 39.052432 87 0 0 33.364337 39.017035 88 0 0 33.316608 38.977429 89 0 0 33.286157 38.951916 90 0 0 33.245993 38.914551 91 0 0 33.200826 38.875494 92 0 0 33.153704 38.837346 93 0 0 33.116104 38.807232 94 0 0 33.085364 38.779526 95 0 0 33.062082 38.759747 96 0 0 33.044471 38.744044 97 0 0 33.028222 38.731696 98 0 0 33.040831 38.740053 99 0 0 33.050746 38.748435 100 0 0 33.076659 38.769493 101 0 0 33.110262 38.796193 102 0 0 33.155559 38.828308 103 0 0 33.189466 38.856863 104 0 0 33.215302 38.872746 105 0 0 33.245413 38.889599 106 0 0 33.244956 38.885565 107 0 0 33.236568 38.87952 108 0 0 33.227224 38.873353 109 0 0 33.204659 38.854053 110 0 0 33.180961 38.837124 111 0 0 33.154726 38.815294 112 0 0 33.097744 38.76795 113 0 0 33.048565 38.728936 114 0 0 33.001577 38.689836 115 0 0 32.939369 38.638983 116 0 0 32.9112 38.617655 117 0 0 32.911419 38.619406 118 0 0 32.895597 38.60739 119 0 0 32.887499 38.603268 120 0 0 32.90813 38.623729 121 0 0 32.90775 38.623682 122 0 0 32.924199 38.632582 123 0 0 32.937925 38.642756 124 0 0 32.949444 38.646456 125 0 0 32.963768 38.652802 126 0 0 32.976767 38.661242 127 0 0 32.975124 38.652734 128 0 0 32.961087 38.643396 129 0 0 32.938964 38.624545 130 0 0 32.914591 38.599057 131 0 0 32.894303 38.586091 132 0 0 32.884027 38.575276 133 0 0 32.868213 38.562261 134 0 0 32.874627 38.56689 135 0 0 32.858704 38.552615 136 0 0 32.856828 38.548942 137 0 0 32.849783 38.545871 138 0 0 32.847841 38.541373 139 0 0 32.866183 38.560233 140 0 0 32.888091 38.577485 141 0 0 32.893288 38.580243 142 0 0 32.923921 38.605664 143 0 0 32.936017 38.617636 144 0 0 32.927857 38.605252 145 0 0 32.920942 38.59689 146 0 0 32.904839 38.582083 147 0 0 32.865944 38.547444 148 0 0 32.838552 38.522864 149 0 0 32.821833 38.511692 150 0 0 32.779628 38.477189 151 0 0 32.752868 38.454093 152 0 0 32.730213 38.43772 153 0 0 32.738966 38.446639 154 0 0 32.732715 38.441112 155 0 0 32.743884 38.448389 156 0 0 32.756508 38.455049 157 0 0 32.789524 38.488882 158 0 0 32.800119 38.491065 159 0 0 32.856688 38.531524 160 0 0 32.890751 38.557715 161 0 0 32.91352 38.579893 162 0 0 32.937018 38.598037 163 0 0 32.977817 38.629765 164 0 0 32.992793 38.648633 165 0 0 32.998065 38.648461 166 0 0 32.99694 38.644311 167 0 0 32.994238 38.640286 168 0 0 32.963504 38.60837 169 0 0 32.919387 38.574927 170 0 0 32.914877 38.571414 171 0 0 32.892741 38.5461 172 0 0 32.904836 38.560244 173 0 0 32.902567 38.563939 174 0 0 32.898297 38.556274 175 0 0 32.926848 38.58195 176 0 0 32.952342 38.609286 177 0 0 32.959501 38.616685 178 0 0 32.9996 38.644706 179 0 0 33.027857 38.678015 180 0 0 33.070155 38.708095 181 0 0 33.128319 38.753158 182 0 0 33.153479 38.780067 183 0 0 33.205201 38.825559 184 0 0 33.213505 38.83696 185 0 0 33.266522 38.87357 186 0 0 33.26844 38.875924 187 0 0 33.313571 38.91049 188 0 0 33.32324 38.920668 189 0 0 33.323128 38.921729 190 0 0 33.31426 38.918001 191 0 0 33.337873 38.938665 192 0 0 33.310007 38.923655 193 0 0 33.272663 38.893344 194 0 0 33.283688 38.911551 195 0 0 33.279155 38.913479 196 0 0 33.262571 38.902484 197 0 0 33.261089 38.904564 198 0 0 33.231885 38.884614 199 0 0 33.249552 38.913238 200 0 0 33.242249 38.913091 201 0 0 33.24229 38.915689 202 0 0 33.251161 38.932081 203 0 0 33.211871 38.908071 204 0 0 33.207117 38.902614 205 0 0 33.179515 38.892795 206 0 0 33.129551 38.857465 207 0 0 33.158192 38.87993 208 0 0 33.135914 38.8703 209 0 0 33.13312 38.868993 210 0 0 33.06924 38.825626 211 0 0 33.09564 38.847994 212 0 0 33.081732 38.839474 213 0 0 33.061082 38.828902 214 0 0 32.978849 38.777012 215 0 0 32.985494 38.787382 216 0 0 32.992376 38.786811 217 0 0 32.946747 38.760101 218 0 0 32.928107 38.756859 219 0 0 32.920167 38.754075 220 0 0 32.892382 38.73647 221 0 0 32.857318 38.702055 222 0 0 32.84512 38.704547 223 0 0 32.88797 38.733426 224 0 0 32.820305 38.689569 225 0 0 32.801556 38.675852 226 0 0 32.803535 38.684706 227 0 0 32.779291 38.668343 228 0 0 32.755276 38.655284 229 0 0 32.699393 38.613141 230 0 0 32.719722 38.629469 231 0 0 32.655132 38.584219 232 0 0 32.616157 38.56116 233 0 0 32.588268 38.538724 234 0 0 32.559918 38.533672 235 0 0 32.568858 38.537996 236 0 0 32.576074 38.535583 237 0 0 32.551099 38.518881 238 0 0 32.445542 38.437289 239 0 0 32.467039 38.466747 240 0 0 32.400011 38.432924 241 0 0 32.419653 38.451765 242 0 0 32.349591 38.396468 243 0 0 32.315354 38.368694 244 0 0 32.364763 38.414659 245 0 0 32.267432 38.344688 246 0 0 32.28204 38.351979 247 0 0 32.211469 38.307231 248 0 0 32.195391 38.303731 249 0 0 32.151853 38.273984 250 0 0 32.185371 38.294552 251 0 0 32.105549 38.248539 252 0 0 32.018474 38.182453 253 0 0 31.982894 38.168995 254 0 0 31.903956 38.099043 255 0 0 31.89754 38.101771 256 0 0 31.855616 38.088745 257 0 0 31.897808 38.103419 258 0 0 31.817481 38.038717 259 0 0 31.782747 38.025617 260 0 0 31.721904 37.996282 261 0 0 31.689841 37.982884 262 0 0 31.668253 37.956669 263 0 0 31.571985 37.900091 264 0 0 31.652342 37.962074 265 0 0 31.554624 37.894098 266 0 0 31.429255 37.805254 267 0 0 31.36483 37.766385 268 0 0 31.349142 37.758152 269 0 0 31.260453 37.705568 270 0 0 31.245419 37.687351 271 0 0 31.243659 37.693597 272 0 0 31.232941 37.701971 273 0 0 30.997569 37.525171 274 0 0 31.04145 37.570342 275 0 0 30.966507 37.47439 276 0 0 30.851668 37.446403 277 0 0 30.826025 37.412774 278 0 0 30.669331 37.279078 279 0 0 30.592482 37.248604 280 0 0 30.545317 37.212598 281 0 0 30.636089 37.275265 282 0 0 30.323217 37.056907 283 0 0 30.360154 37.122829 284 0 0 30.256916 37.001386 285 0 0 30.17023 36.940963 286 0 0 30.00666 36.861394 287 0 0 30.081784 36.882156 288 0 0 30.113963 36.908798 289 0 0 29.919299 36.791389 290 0 0 29.823389 36.712635 291 0 0 29.753374 36.665875 292 0 0 29.692099 36.629467 293 0 0 29.658554 36.603089 294 0 0 29.619855 36.622214 295 0 0 29.495244 36.462894 296 0 0 29.557774 36.498592 297 0 0 29.337492 36.382828 298 0 0 29.273663 36.348162 299 0 0 29.263652 36.321906 300 0 0 29.107243 36.19667 301 0 0 29.085422 36.236229 302 0 0 29.059839 36.217534 303 0 0 28.936325 36.11835 304 0 0 28.896391 36.085847 305 0 0 28.81761 36.03504 306 0 0 28.995718 36.192916 307 0 0 28.896563 36.0885 308 0 0 28.769355 35.942459 309 0 0 28.518356 35.785936 310 0 0 28.498598 35.776932 311 0 0 28.545962 35.841137 312 0 0 28.698624 35.900765 313 0 0 28.403617 35.676743 314 0 0 28.639082 35.854422 315 0 0 28.526665 35.849236 316 0 0 28.672398 35.831197 317 0 0 28.346766 35.694209 318 0 0 28.198895 35.570657 319 0 0 28.347686 35.628974 320 0 0 28.391821 35.683817 321 0 0 27.911208 35.25182 322 0 0 28.134185 35.495208 323 0 0 27.877297 35.322664 324 0 0 28.194408 35.542913 325 0 0 28.231812 35.636234 326 0 0 27.5752 35.063733 327 0 0 28.121294 35.483378 328 0 0 27.924227 35.304088 329 0 0 28.109357 35.4705 330 0 0 27.65443 35.118987 331 0 0 27.830084 35.114206 332 0 0 27.742089 35.363924 333 0 0 27.989286 35.390476 334 0 0 27.819838 35.302294 335 0 0 27.653846 35.220211 336 0 0 28.126316 35.407895 337 0 0 28.077381 35.507937 338 0 0 27.708054 35.246085 339 0 0 27.397112 34.802647 340 0 0 27.19917 34.829876 341 0 0 26.725962 34.459936 342 0 0 27.188172 35.001792 343 0 0 27.048193 34.566265 344 0 0 27.458904 34.96347 345 0 0 27.923664 35.676845 346 0 0 27.486239 35.149847 347 0 0 25.395833 33.9375 348 0 0 27.5 34.868217 349 0 0 28.445946 35.981982 350 0 0 25.78125 34.213542 351 0 0 25.759259 34.049383 352 0 0 25.666667 33.881944 353 0 0 29.325581 36.651163 354 0 0 26.135135 33.774775 355 0 0 26.59375 34.020833 356 0 0 26.333333 34.222222 357 0 0 28.708333 35.833333 358 0 0 28.9 36.3 359 0 0 24.235294 32.843137 360 0 0 25.6 33 361 0 0 25.571429 33.02381 362 0 0 24.777778 33.592593 363 0 0 25.666667 35.074074 364 0 0 24.555556 33.333333 365 0 0 24.5 33.083333 366 0 0 30.857143 37.238095 367 0 0 22.857143 31.52381 368 0 0 26.857143 35.666667 369 0 0 28.666667 36.611111 370 0 0 22.6 33.4 371 0 0 22 30.133333 372 0 0 22 29.066667 373 0 0 28.4 35.666667 374 0 0 27.25 33.25 375 0 0 21.75 30 376 0 0 28.75 37.416667 377 0 0 30.5 37.166667 378 0 0 34.333333 40 379 0 0 22.5 31 380 0 0 35 40 381 0 0 18 23.666667 382 0 0 36 41 383 0 0 24 32.333333 384 0 0 18 33.333333 385 0 0 34 39.666667 386 0 0 5 23.333333