## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5407-Z0097-CAGTCAGTTGCAGAT/441525-L5407-Z0097-CAGTCAGTTGCAGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5407-Z0097-CAGTCAGTTGCAGAT/441525-L5407-Z0097-CAGTCAGTTGCAGAT_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 1000566 1000566 132 132355023 132355023 127394517 127394517 118195473 118195473 0 0 0.962521 0.893018 0 0.962521 0.893018 0 397065069 397065069 390500513 390500513 375746069 375746069 351106478 351106478 0.983467 0.946309 0.884254 0.983467 0.946309 0.884254 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 888 1 35.994397 40.995847 1 11755 0 35.987778 40.991648 2 13834 4629 35.994479 40.995462 3 35554 1298 35.981809 40.98515 4 56904 50185 35.991138 40.992741 5 114619 18559 35.995027 40.99585 6 110786 128649 35.975816 40.979573 7 198409 162622 35.975959 40.983597 8 194596 150279 35.986514 40.988939 9 244452 113563 35.958179 40.964748 10 255607 509364 35.886624 40.930124 11 305068 63848 35.925132 40.944957 12 360377 716480 35.210704 40.336813 13 355827 213871 33.711924 39.580352 14 470943 1012570 35.88878 40.933074 15 377109 382418 35.795845 40.854237 16 395844 449245 35.752353 40.77747 17 523192 1132309 35.885409 40.902501 18 561310 743375 35.736275 40.784135 19 373432 711291 35.73423 40.805496 20 511851 1007260 35.900515 40.9349 21 663978 1388344 35.830414 40.876644 22 325403 560460 35.5989 40.721241 23 1041096 1211317 35.291282 40.506019 24 584777 1204053 35.287142 40.510276 25 544276 473026 35.294955 40.518334 26 1762363 2554123 35.234122 40.470849 27 363838 877313 35.238623 40.481561 28 953960 386222 35.253319 40.492393 29 2447502 5092326 35.246052 40.484941 30 759912 41933 35.249779 40.487572 31 2316490 813113 35.23874 40.478301 32 1625691 5472731 35.224865 40.466069 33 838997 126898 35.234525 40.474623 34 2433669 2671956 35.223484 40.469058 35 2194569 3815630 35.240905 40.480887 36 108026145 2120365 35.261793 40.496002 37 0 4214988 35.268382 40.501138 38 0 391612 35.259847 40.495139 39 0 4970365 35.264557 40.498571 40 0 0 35.250352 40.487626 41 0 351106478 35.239565 40.479159 42 0 0 35.232246 40.473931 43 0 0 35.234142 40.474868 44 0 0 35.238378 40.478506 45 0 0 35.242305 40.480121 46 0 0 35.233421 40.473806 47 0 0 35.22729 40.468136 48 0 0 35.212607 40.459076 49 0 0 35.210051 40.456772 50 0 0 35.200128 40.450984 51 0 0 35.195787 40.446968 52 0 0 35.166112 40.426171 53 0 0 35.139363 40.406873 54 0 0 35.131018 40.398539 55 0 0 35.109241 40.381221 56 0 0 35.070853 40.355784 57 0 0 35.085018 40.365835 58 0 0 35.055237 40.341077 59 0 0 35.008784 40.307899 60 0 0 34.978419 40.293076 61 0 0 34.944731 40.265876 62 0 0 34.90204 40.230842 63 0 0 34.858474 40.19803 64 0 0 34.803725 40.15565 65 0 0 34.74518 40.113185 66 0 0 34.694567 40.07687 67 0 0 34.633738 40.031258 68 0 0 34.552374 39.971815 69 0 0 34.471441 39.91016 70 0 0 34.373511 39.833101 71 0 0 34.267052 39.750048 72 0 0 34.155843 39.661692 73 0 0 34.055344 39.57819 74 0 0 33.940246 39.488131 75 0 0 33.82972 39.399469 76 0 0 33.729337 39.324864 77 0 0 33.607303 39.234239 78 0 0 33.497551 39.151215 79 0 0 33.391591 39.064493 80 0 0 33.286599 38.981642 81 0 0 33.210231 38.919961 82 0 0 33.140071 38.859682 83 0 0 33.075035 38.805919 84 0 0 33.00791 38.753063 85 0 0 32.950812 38.707945 86 0 0 32.905246 38.669872 87 0 0 32.864321 38.636319 88 0 0 32.809464 38.587415 89 0 0 32.759256 38.545092 90 0 0 32.72014 38.510194 91 0 0 32.671209 38.465651 92 0 0 32.638388 38.437934 93 0 0 32.616548 38.414399 94 0 0 32.595914 38.393094 95 0 0 32.566976 38.370205 96 0 0 32.55485 38.360589 97 0 0 32.533027 38.338639 98 0 0 32.548715 38.35441 99 0 0 32.56786 38.36831 100 0 0 32.596927 38.390039 101 0 0 32.641944 38.423453 102 0 0 32.690923 38.45856 103 0 0 32.733193 38.490575 104 0 0 32.748293 38.497936 105 0 0 32.779078 38.521717 106 0 0 32.80318 38.536936 107 0 0 32.809218 38.538786 108 0 0 32.826335 38.554117 109 0 0 32.832135 38.560097 110 0 0 32.813079 38.546423 111 0 0 32.789776 38.527616 112 0 0 32.758145 38.496215 113 0 0 32.716661 38.460796 114 0 0 32.662554 38.417132 115 0 0 32.634875 38.397575 116 0 0 32.599994 38.368186 117 0 0 32.595181 38.369964 118 0 0 32.589498 38.368144 119 0 0 32.588439 38.371762 120 0 0 32.617788 38.39349 121 0 0 32.648117 38.416742 122 0 0 32.663764 38.428212 123 0 0 32.67329 38.433001 124 0 0 32.701806 38.452741 125 0 0 32.732734 38.480473 126 0 0 32.744186 38.478244 127 0 0 32.776631 38.501961 128 0 0 32.764084 38.484337 129 0 0 32.743688 38.470435 130 0 0 32.729578 38.461844 131 0 0 32.738167 38.460539 132 0 0 32.720581 38.446942 133 0 0 32.720864 38.448646 134 0 0 32.718475 38.446777 135 0 0 32.712904 38.432084 136 0 0 32.714655 38.440384 137 0 0 32.698675 38.426101 138 0 0 32.69483 38.42127 139 0 0 32.729825 38.451506 140 0 0 32.753 38.471281 141 0 0 32.778054 38.4898 142 0 0 32.784692 38.496757 143 0 0 32.807154 38.511678 144 0 0 32.804269 38.509964 145 0 0 32.806913 38.505712 146 0 0 32.795685 38.496135 147 0 0 32.749308 38.453135 148 0 0 32.710902 38.421338 149 0 0 32.697683 38.40585 150 0 0 32.650715 38.370253 151 0 0 32.623962 38.352623 152 0 0 32.586424 38.321325 153 0 0 32.591599 38.328942 154 0 0 32.587001 38.32504 155 0 0 32.566615 38.308196 156 0 0 32.589354 38.322582 157 0 0 32.583494 38.319653 158 0 0 32.636781 38.359531 159 0 0 32.667969 38.37951 160 0 0 32.688138 38.397722 161 0 0 32.720223 38.422059 162 0 0 32.742113 38.437909 163 0 0 32.780455 38.477027 164 0 0 32.772136 38.462259 165 0 0 32.770449 38.458295 166 0 0 32.779448 38.465195 167 0 0 32.761286 38.444401 168 0 0 32.714311 38.394554 169 0 0 32.692172 38.381903 170 0 0 32.613595 38.312511 171 0 0 32.594532 38.29989 172 0 0 32.575614 38.288933 173 0 0 32.605243 38.310521 174 0 0 32.592944 38.299534 175 0 0 32.612928 38.317727 176 0 0 32.64103 38.344231 177 0 0 32.674268 38.368849 178 0 0 32.710767 38.4026 179 0 0 32.741196 38.427661 180 0 0 32.795218 38.474474 181 0 0 32.836565 38.509831 182 0 0 32.883824 38.553283 183 0 0 32.954852 38.599054 184 0 0 32.97679 38.622178 185 0 0 33.00264 38.645621 186 0 0 33.027402 38.668057 187 0 0 33.067567 38.700674 188 0 0 33.086235 38.70995 189 0 0 33.081439 38.711461 190 0 0 33.068819 38.701513 191 0 0 33.101324 38.736205 192 0 0 33.046171 38.697301 193 0 0 33.002048 38.664062 194 0 0 32.975557 38.657822 195 0 0 32.982892 38.656192 196 0 0 33.005312 38.682127 197 0 0 32.969522 38.662769 198 0 0 32.951701 38.654863 199 0 0 32.957444 38.668349 200 0 0 32.933163 38.652027 201 0 0 32.955592 38.678259 202 0 0 32.923397 38.662796 203 0 0 32.956488 38.690982 204 0 0 32.889382 38.652199 205 0 0 32.89089 38.656138 206 0 0 32.893364 38.66387 207 0 0 32.84365 38.6269 208 0 0 32.829992 38.6308 209 0 0 32.792989 38.600002 210 0 0 32.781762 38.606667 211 0 0 32.790656 38.608283 212 0 0 32.72973 38.561605 213 0 0 32.708323 38.557782 214 0 0 32.692411 38.550004 215 0 0 32.654513 38.517 216 0 0 32.673413 38.533495 217 0 0 32.642115 38.53111 218 0 0 32.60158 38.486926 219 0 0 32.615349 38.512541 220 0 0 32.591116 38.492573 221 0 0 32.559383 38.467406 222 0 0 32.558198 38.471823 223 0 0 32.541435 38.471226 224 0 0 32.580643 38.486723 225 0 0 32.559925 38.488814 226 0 0 32.467395 38.418897 227 0 0 32.498686 38.429746 228 0 0 32.438603 38.37761 229 0 0 32.499107 38.424773 230 0 0 32.441651 38.405395 231 0 0 32.421429 38.401334 232 0 0 32.389714 38.401327 233 0 0 32.379812 38.37715 234 0 0 32.35531 38.331278 235 0 0 32.384221 38.360719 236 0 0 32.335617 38.338602 237 0 0 32.255427 38.304261 238 0 0 32.17863 38.229906 239 0 0 32.264393 38.315655 240 0 0 32.190011 38.242816 241 0 0 32.179674 38.249442 242 0 0 32.08717 38.200173 243 0 0 32.175584 38.243784 244 0 0 32.081174 38.189823 245 0 0 32.081063 38.208505 246 0 0 32.06075 38.162553 247 0 0 32.077486 38.219599 248 0 0 32.061366 38.171231 249 0 0 32.063144 38.169005 250 0 0 32.057903 38.169536 251 0 0 31.818683 38.023536 252 0 0 31.811421 38.005625 253 0 0 31.9328 38.109571 254 0 0 31.720214 37.940515 255 0 0 31.958451 38.131285 256 0 0 31.625796 37.89285 257 0 0 31.701407 37.950811 258 0 0 31.705756 37.972788 259 0 0 31.755909 38.001796 260 0 0 31.705489 37.98612 261 0 0 31.619413 37.91593 262 0 0 31.756065 37.993433 263 0 0 31.686388 37.962626 264 0 0 31.482587 37.811988 265 0 0 31.311762 37.686926 266 0 0 31.425258 37.802235 267 0 0 31.468118 37.812232 268 0 0 31.323608 37.715085 269 0 0 31.226549 37.643336 270 0 0 31.417655 37.79798 271 0 0 31.227012 37.633266 272 0 0 31.148467 37.631818 273 0 0 30.965827 37.500617 274 0 0 31.064255 37.545416 275 0 0 30.896877 37.419331 276 0 0 30.946212 37.452273 277 0 0 30.799884 37.374492 278 0 0 30.522498 37.237859 279 0 0 30.530712 37.211433 280 0 0 30.509767 37.18156 281 0 0 30.351415 37.098277 282 0 0 30.2934 37.094751 283 0 0 30.241119 37.002072 284 0 0 29.976337 36.809784 285 0 0 30.233396 37.075226 286 0 0 29.945084 36.806395 287 0 0 29.986726 36.832842 288 0 0 29.853739 36.761724 289 0 0 29.748497 36.637996 290 0 0 29.673041 36.640991 291 0 0 29.649055 36.603263 292 0 0 29.380416 36.391296 293 0 0 29.541047 36.500099 294 0 0 29.415333 36.453305 295 0 0 29.079396 36.268617 296 0 0 29.11063 36.276797 297 0 0 29.32812 36.392654 298 0 0 29.341712 36.331512 299 0 0 29.011086 36.12895 300 0 0 29.236139 36.330009 301 0 0 29.0189 36.153297 302 0 0 28.930641 36.0518 303 0 0 28.791513 35.980781 304 0 0 28.81351 36.013379 305 0 0 28.55413 35.867624 306 0 0 28.707264 35.98398 307 0 0 28.351163 35.681977 308 0 0 28.753704 35.978807 309 0 0 28.727213 35.940114 310 0 0 28.218661 35.558642 311 0 0 28.400153 35.770977 312 0 0 28.626743 35.899918 313 0 0 28.050863 35.436876 314 0 0 28.641051 35.788262 315 0 0 28.289417 35.573794 316 0 0 28.536952 35.797152 317 0 0 28.14717 35.490985 318 0 0 28.20191 35.566166 319 0 0 28.3789 35.687964 320 0 0 28.281804 35.672034 321 0 0 28.842294 36.132019 322 0 0 28.877712 35.874425 323 0 0 27.678801 35.391863 324 0 0 27.767386 35.445244 325 0 0 28.258152 35.574275 326 0 0 27.847305 35.006986 327 0 0 28.408497 35.742919 328 0 0 27.312057 34.820331 329 0 0 28.272 35.646667 330 0 0 27.728507 35.236802 331 0 0 27.311881 35.082508 332 0 0 27.632979 35.338652 333 0 0 28.035928 35.239521 334 0 0 26.310811 34.443694 335 0 0 27.186567 34.855721 336 0 0 28.504065 35.853659 337 0 0 26.962617 34.520249 338 0 0 28.568421 36.168421 339 0 0 27.441558 35.316017 340 0 0 28.028571 35.357143 341 0 0 28.516667 35.444444 342 0 0 27.2 34.333333 343 0 0 26.653846 34.75641 344 0 0 30.041667 36.951389 345 0 0 27.974359 35.803419 346 0 0 27.529412 35.77451 347 0 0 24.21875 32.729167 348 0 0 25.571429 33.011905 349 0 0 29.086957 36.753623 350 0 0 27.761905 35.650794 351 0 0 29.952381 37.380952 352 0 0 26.666667 34.488889 353 0 0 26.727273 34.484848 354 0 0 28.875 36.166667 355 0 0 24.428571 31.285714 356 0 0 22.166667 30.388889 357 0 0 32.25 37.416667 358 0 0 27.25 37.25 359 0 0 26.5 35.75 360 0 0 25.666667 36.222222 361 0 0 22 31.444444 362 0 0 36 41 363 0 0 32 38 364 0 0 30.5 38.5 365 0 0 18 27.833333 366 0 0 25 33.333333 367 0 0 30 38.166667 368 0 0 9 18.833333 369 0 0 29.5 36 370 0 0 16.5 28.166667 371 0 0 16.5 26.666667 372 0 0 20.5 29.333333 373 0 0 24 32.333333 374 0 0 19.5 29.333333 375 0 0 27 35.5 376 0 0 25.5 34.166667 377 0 0 18 32.666667