## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5278-Z0020-CTACATTGCACAGAT/441525-L5278-Z0020-CTACATTGCACAGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5278-Z0020-CTACATTGCACAGAT/441525-L5278-Z0020-CTACATTGCACAGAT_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 03:00:15 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 999717 999717 184 184065218 184065218 179246946 179246946 169374031 169374031 0 0 0.973823 0.920185 0 0.973823 0.920185 0 552195654 552195654 545984760 545984760 530539288 530539288 503892617 503892617 0.988752 0.960781 0.912526 0.988752 0.960781 0.912526 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 1158 0 35.992536 40.994383 1 15525 0 35.985475 40.989958 2 18782 7621 35.994235 40.995195 3 44778 1937 35.981029 40.984815 4 64288 62296 35.989386 40.991462 5 133600 16972 35.994905 40.99578 6 98001 162834 35.969241 40.976167 7 216747 188463 35.980004 40.986306 8 168450 153619 35.98668 40.989151 9 244554 122054 35.904821 40.919619 10 251540 502689 35.905529 40.933434 11 295410 73653 35.941445 40.959283 12 335935 689761 35.629392 40.691473 13 318105 201550 34.78134 40.251404 14 456667 927176 35.875994 40.927397 15 381199 390650 35.666034 40.765749 16 348004 360504 35.636889 40.675442 17 502716 985903 35.887246 40.90755 18 544765 736647 35.669265 40.738302 19 378048 626565 35.797825 40.85231 20 600821 920592 35.935426 40.95606 21 685537 1405419 35.837912 40.883237 22 377851 505460 35.643698 40.759763 23 1289399 1559098 35.41492 40.608522 24 610599 1250001 35.451884 40.626549 25 546078 512005 35.431456 40.613859 26 1918086 2754391 35.398915 40.590088 27 374387 990739 35.418367 40.608198 28 945497 446302 35.417445 40.607254 29 2524660 5101465 35.412309 40.602631 30 856160 57570 35.40864 40.599557 31 2565285 1110502 35.395788 40.591498 32 1956239 5232968 35.393419 40.587497 33 968943 168994 35.39564 40.590164 34 2754419 3302139 35.3861 40.584407 35 2573005 3706820 35.402495 40.595539 36 157699980 2814539 35.422859 40.608436 37 0 4204767 35.412779 40.603279 38 0 629464 35.407924 40.601354 39 0 5418908 35.405067 40.599434 40 0 13 35.401645 40.594691 41 0 503892604 35.386172 40.583822 42 0 0 35.377231 40.578706 43 0 0 35.381231 40.580427 44 0 0 35.391246 40.586928 45 0 0 35.392102 40.587349 46 0 0 35.385993 40.583994 47 0 0 35.380277 40.581204 48 0 0 35.38269 40.581685 49 0 0 35.370529 40.572252 50 0 0 35.368396 40.571532 51 0 0 35.363556 40.568257 52 0 0 35.359092 40.565206 53 0 0 35.351263 40.560809 54 0 0 35.353143 40.561541 55 0 0 35.346212 40.558362 56 0 0 35.335194 40.549939 57 0 0 35.327535 40.544025 58 0 0 35.322173 40.537921 59 0 0 35.309084 40.529674 60 0 0 35.300669 40.521474 61 0 0 35.279211 40.506607 62 0 0 35.264514 40.495473 63 0 0 35.242708 40.478024 64 0 0 35.223307 40.464235 65 0 0 35.203109 40.448228 66 0 0 35.177723 40.429942 67 0 0 35.14957 40.409344 68 0 0 35.123276 40.389539 69 0 0 35.096736 40.368407 70 0 0 35.062416 40.342363 71 0 0 35.03105 40.316876 72 0 0 34.999057 40.290212 73 0 0 34.961731 40.261532 74 0 0 34.930085 40.238059 75 0 0 34.897618 40.211836 76 0 0 34.85955 40.182265 77 0 0 34.83169 40.161087 78 0 0 34.79565 40.132278 79 0 0 34.765286 40.108089 80 0 0 34.731661 40.08101 81 0 0 34.696151 40.051795 82 0 0 34.667928 40.028663 83 0 0 34.64048 40.007423 84 0 0 34.611375 39.984266 85 0 0 34.599514 39.972745 86 0 0 34.582528 39.958331 87 0 0 34.55306 39.935045 88 0 0 34.538009 39.921849 89 0 0 34.52297 39.912534 90 0 0 34.504181 39.89501 91 0 0 34.495714 39.886482 92 0 0 34.483928 39.874587 93 0 0 34.480757 39.869741 94 0 0 34.458869 39.853442 95 0 0 34.448411 39.84231 96 0 0 34.45002 39.843622 97 0 0 34.434984 39.832112 98 0 0 34.430105 39.82728 99 0 0 34.439959 39.837021 100 0 0 34.442891 39.835537 101 0 0 34.445599 39.839417 102 0 0 34.45278 39.841446 103 0 0 34.459097 39.847342 104 0 0 34.472127 39.85627 105 0 0 34.478135 39.8601 106 0 0 34.486527 39.864171 107 0 0 34.490857 39.87081 108 0 0 34.504398 39.880913 109 0 0 34.504796 39.880848 110 0 0 34.5131 39.886721 111 0 0 34.508794 39.885013 112 0 0 34.499667 39.875645 113 0 0 34.490728 39.867981 114 0 0 34.474953 39.852904 115 0 0 34.464855 39.843636 116 0 0 34.460482 39.841584 117 0 0 34.449935 39.83326 118 0 0 34.45429 39.839941 119 0 0 34.448727 39.835647 120 0 0 34.448303 39.835907 121 0 0 34.451302 39.838646 122 0 0 34.449541 39.835514 123 0 0 34.452842 39.836504 124 0 0 34.446888 39.831439 125 0 0 34.459082 39.840154 126 0 0 34.463258 39.841097 127 0 0 34.471198 39.848892 128 0 0 34.480292 39.855245 129 0 0 34.476273 39.852521 130 0 0 34.486784 39.861019 131 0 0 34.479636 39.856195 132 0 0 34.480585 39.855551 133 0 0 34.48006 39.853639 134 0 0 34.485154 39.855966 135 0 0 34.475042 39.846877 136 0 0 34.473316 39.845948 137 0 0 34.46394 39.838368 138 0 0 34.469367 39.842467 139 0 0 34.454587 39.834135 140 0 0 34.463577 39.842228 141 0 0 34.479151 39.855419 142 0 0 34.48124 39.856852 143 0 0 34.487318 39.858245 144 0 0 34.478314 39.851186 145 0 0 34.471749 39.846392 146 0 0 34.463853 39.836846 147 0 0 34.442198 39.820279 148 0 0 34.426223 39.80783 149 0 0 34.411415 39.795811 150 0 0 34.391768 39.781216 151 0 0 34.375614 39.767743 152 0 0 34.363578 39.759388 153 0 0 34.356881 39.752173 154 0 0 34.334778 39.736163 155 0 0 34.319351 39.722611 156 0 0 34.305384 39.711967 157 0 0 34.278596 39.687513 158 0 0 34.287094 39.692686 159 0 0 34.267157 39.677938 160 0 0 34.28651 39.692408 161 0 0 34.273655 39.682896 162 0 0 34.256753 39.670825 163 0 0 34.252809 39.667745 164 0 0 34.245466 39.661661 165 0 0 34.227189 39.646549 166 0 0 34.196657 39.621965 167 0 0 34.163891 39.59344 168 0 0 34.107471 39.546735 169 0 0 34.068808 39.514299 170 0 0 34.006158 39.460662 171 0 0 33.954827 39.413227 172 0 0 33.910876 39.379167 173 0 0 33.847118 39.324502 174 0 0 33.816739 39.30335 175 0 0 33.778338 39.26921 176 0 0 33.741903 39.239057 177 0 0 33.710503 39.211551 178 0 0 33.683481 39.189326 179 0 0 33.661948 39.170247 180 0 0 33.646974 39.157604 181 0 0 33.635294 39.149262 182 0 0 33.642929 39.156864 183 0 0 33.634897 39.147037 184 0 0 33.647619 39.16313 185 0 0 33.64824 39.161011 186 0 0 33.671373 39.174972 187 0 0 33.684969 39.187485 188 0 0 33.688079 39.18897 189 0 0 33.690723 39.191607 190 0 0 33.687739 39.188152 191 0 0 33.683809 39.185691 192 0 0 33.687451 39.191223 193 0 0 33.684084 39.191588 194 0 0 33.661545 39.176282 195 0 0 33.656395 39.174173 196 0 0 33.638786 39.166416 197 0 0 33.626525 39.158265 198 0 0 33.61636 39.154202 199 0 0 33.599118 39.144338 200 0 0 33.582855 39.139217 201 0 0 33.547691 39.115966 202 0 0 33.518821 39.101116 203 0 0 33.492607 39.081936 204 0 0 33.475947 39.076744 205 0 0 33.446838 39.060686 206 0 0 33.408896 39.038376 207 0 0 33.372406 39.019217 208 0 0 33.334242 38.993704 209 0 0 33.312102 38.981282 210 0 0 33.2682 38.954144 211 0 0 33.232301 38.937894 212 0 0 33.211561 38.926213 213 0 0 33.190156 38.916276 214 0 0 33.148183 38.89204 215 0 0 33.107485 38.866765 216 0 0 33.071278 38.837619 217 0 0 33.04276 38.825573 218 0 0 33.03043 38.815957 219 0 0 32.974319 38.779045 220 0 0 32.936136 38.753597 221 0 0 32.927511 38.75219 222 0 0 32.884415 38.721047 223 0 0 32.869975 38.711543 224 0 0 32.825812 38.685877 225 0 0 32.794426 38.662689 226 0 0 32.752527 38.632816 227 0 0 32.756251 38.640534 228 0 0 32.736831 38.63354 229 0 0 32.678533 38.594222 230 0 0 32.668912 38.587124 231 0 0 32.651509 38.577431 232 0 0 32.609843 38.551015 233 0 0 32.589526 38.540431 234 0 0 32.556889 38.522913 235 0 0 32.511726 38.49342 236 0 0 32.484646 38.466765 237 0 0 32.479701 38.47135 238 0 0 32.414858 38.424719 239 0 0 32.379581 38.399769 240 0 0 32.35269 38.384622 241 0 0 32.317604 38.368669 242 0 0 32.308708 38.368591 243 0 0 32.252314 38.323974 244 0 0 32.227503 38.314668 245 0 0 32.207467 38.29825 246 0 0 32.172233 38.286507 247 0 0 32.10543 38.234584 248 0 0 32.078918 38.209294 249 0 0 32.060027 38.21681 250 0 0 32.042203 38.200447 251 0 0 32.022312 38.182335 252 0 0 31.956495 38.142855 253 0 0 31.942079 38.137027 254 0 0 31.908487 38.120071 255 0 0 31.8582 38.088452 256 0 0 31.837307 38.07488 257 0 0 31.810714 38.063583 258 0 0 31.751947 38.020213 259 0 0 31.687194 37.978152 260 0 0 31.671439 37.97834 261 0 0 31.615813 37.932598 262 0 0 31.58168 37.915101 263 0 0 31.576653 37.913718 264 0 0 31.529362 37.876563 265 0 0 31.439667 37.824263 266 0 0 31.354886 37.749495 267 0 0 31.394304 37.794395 268 0 0 31.268271 37.704039 269 0 0 31.25633 37.693758 270 0 0 31.152377 37.633597 271 0 0 31.152954 37.64809 272 0 0 31.124369 37.614324 273 0 0 30.9713 37.519312 274 0 0 30.981217 37.533796 275 0 0 30.883915 37.465069 276 0 0 30.886789 37.45324 277 0 0 30.767382 37.372185 278 0 0 30.724348 37.352811 279 0 0 30.605526 37.260214 280 0 0 30.60408 37.27373 281 0 0 30.416497 37.135569 282 0 0 30.41985 37.146115 283 0 0 30.35791 37.088628 284 0 0 30.261507 37.033879 285 0 0 30.214597 37.00763 286 0 0 30.167938 36.96076 287 0 0 30.106381 36.923836 288 0 0 30.065848 36.89395 289 0 0 29.968853 36.840418 290 0 0 29.940768 36.801128 291 0 0 29.89226 36.765298 292 0 0 29.818763 36.725352 293 0 0 29.727165 36.660224 294 0 0 29.684073 36.623856 295 0 0 29.723779 36.664927 296 0 0 29.588952 36.55382 297 0 0 29.568431 36.556911 298 0 0 29.428637 36.457933 299 0 0 29.45795 36.45678 300 0 0 29.418371 36.431984 301 0 0 29.28067 36.358996 302 0 0 29.190012 36.279955 303 0 0 29.226253 36.297512 304 0 0 29.113029 36.234603 305 0 0 29.17461 36.277489 306 0 0 29.045552 36.179138 307 0 0 29.020688 36.169584 308 0 0 28.962565 36.122498 309 0 0 28.955396 36.090341 310 0 0 28.944617 36.103295 311 0 0 28.926369 36.076404 312 0 0 28.890928 36.067567 313 0 0 28.78638 36.009688 314 0 0 28.769625 35.98575 315 0 0 28.824155 35.998884 316 0 0 28.857429 36.037052 317 0 0 28.709889 35.919519 318 0 0 28.749907 35.952555 319 0 0 28.733475 35.975807 320 0 0 28.510146 35.731767 321 0 0 28.590811 35.845689 322 0 0 28.588823 35.86899 323 0 0 28.490173 35.798603 324 0 0 28.601872 35.870041 325 0 0 28.714485 35.88662 326 0 0 28.414442 35.701556 327 0 0 28.614698 35.830076 328 0 0 28.24935 35.659891 329 0 0 28.476165 35.785708 330 0 0 28.40921 35.675605 331 0 0 27.888961 35.355259 332 0 0 28.145044 35.519922 333 0 0 28.45971 35.73422 334 0 0 28.673561 35.923261 335 0 0 28.311178 35.677241 336 0 0 28.166667 35.622298 337 0 0 28.254226 35.59016 338 0 0 28.135667 35.393873 339 0 0 27.903465 35.327558 340 0 0 28.477064 35.851376 341 0 0 28.658174 35.917197 342 0 0 27.832732 35.292018 343 0 0 28.461853 35.898274 344 0 0 27.722662 35.34654 345 0 0 27.850277 35.338262 346 0 0 27.559574 35.092199 347 0 0 26.797561 34.496748 348 0 0 27.851541 35.337068 349 0 0 27.160656 34.723497 350 0 0 27.76779 35.398252 351 0 0 27.512821 35.2849 352 0 0 28.135922 35.644013 353 0 0 27.431818 34.914773 354 0 0 27.535484 34.954839 355 0 0 28.933333 36.192593 356 0 0 27.720339 35.048023 357 0 0 27.989899 35.710438 358 0 0 26.873563 34.605364 359 0 0 28.88 35.826667 360 0 0 30.149254 37.358209 361 0 0 28.473684 35.935673 362 0 0 27.6 35.273333 363 0 0 30.06383 37.170213 364 0 0 26.651163 35.271318 365 0 0 30.692308 37.42735 366 0 0 25.424242 33.666667 367 0 0 28.862069 36.183908 368 0 0 28.48 34.546667 369 0 0 30 37.318182 370 0 0 29.388889 36.981481 371 0 0 29.176471 35.45098 372 0 0 31.8 38.133333 373 0 0 32.230769 38.410256 374 0 0 31.272727 37.363636 375 0 0 32.625 38.583333 376 0 0 35.125 40.416667 377 0 0 31.375 37.333333 378 0 0 26.75 34 379 0 0 28.625 36 380 0 0 28.285714 35.666667 381 0 0 28 36.833333 382 0 0 26.666667 34.944444 383 0 0 27.6 35.2 384 0 0 27.75 35.166667 385 0 0 27 34.666667 386 0 0 36 41 387 0 0 36 41 388 0 0 36 41 389 0 0 36 41 390 0 0 36 41 391 0 0 36 41