## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5397-Z0085-CTCTATGTTGCTGAT/441525-L5397-Z0085-CTCTATGTTGCTGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5397-Z0085-CTCTATGTTGCTGAT/441525-L5397-Z0085-CTCTATGTTGCTGAT_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 03:02:03 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 1000964 1000964 126 126966011 126966011 122195184 122195184 113188963 113188963 0 0 0.962424 0.89149 0 0.962424 0.89149 0 380898033 380898033 374554315 374554315 360209550 360209550 336182264 336182264 0.983345 0.945685 0.882604 0.983345 0.945685 0.882604 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 796 0 35.993917 40.995316 1 10075 0 35.984457 40.989466 2 12393 3998 35.992056 40.993384 3 31369 1061 35.976758 40.981233 4 52608 43016 35.990071 40.992021 5 102104 15986 35.994365 40.995411 6 110047 112515 35.963311 40.967811 7 182338 145174 35.970697 40.979344 8 189831 141472 35.988657 40.990725 9 226525 100201 35.962231 40.96835 10 240936 492920 35.836408 40.906339 11 286017 55262 35.891192 40.917445 12 345732 686955 35.131751 40.277262 13 348279 203569 33.528398 39.472494 14 451825 981949 35.861638 40.914658 15 364269 363037 35.840049 40.885981 16 389611 456686 35.781921 40.807247 17 512484 1120013 35.890876 40.906176 18 546837 703768 35.732391 40.782162 19 366751 716136 35.738458 40.807697 20 489181 1013661 35.899625 40.933872 21 640216 1323738 35.843279 40.887097 22 312795 565642 35.622047 40.74241 23 1005040 1151314 35.350849 40.553704 24 553189 1130929 35.359295 40.56589 25 530243 465093 35.365913 40.570635 26 1736499 2480296 35.296588 40.518527 27 343751 836098 35.308881 40.531078 28 950600 353783 35.320811 40.540951 29 2444707 5024211 35.323763 40.539789 30 727497 38390 35.324376 40.540882 31 2289600 757690 35.317965 40.534583 32 1509837 5433099 35.312664 40.529602 33 804712 116046 35.30831 40.528988 34 2389947 2415851 35.298031 40.521824 35 2160424 3854413 35.313183 40.531484 36 103306946 1931637 35.332184 40.544851 37 0 4257242 35.333956 40.545816 38 0 341834 35.322415 40.53995 39 0 4881084 35.317762 40.535414 40 0 0 35.31995 40.537124 41 0 336182264 35.29739 40.520556 42 0 0 35.294863 40.51792 43 0 0 35.297325 40.519826 44 0 0 35.305257 40.524459 45 0 0 35.30551 40.524218 46 0 0 35.299032 40.51914 47 0 0 35.292761 40.515615 48 0 0 35.27491 40.504152 49 0 0 35.276241 40.503693 50 0 0 35.265719 40.497677 51 0 0 35.261761 40.494703 52 0 0 35.237249 40.477221 53 0 0 35.212901 40.459648 54 0 0 35.210776 40.456288 55 0 0 35.180486 40.43233 56 0 0 35.146023 40.410502 57 0 0 35.134102 40.403051 58 0 0 35.087344 40.365375 59 0 0 35.046947 40.337808 60 0 0 34.988632 40.299119 61 0 0 34.929691 40.250825 62 0 0 34.86141 40.196972 63 0 0 34.786993 40.139984 64 0 0 34.695536 40.069024 65 0 0 34.593788 39.994866 66 0 0 34.50402 39.927479 67 0 0 34.395503 39.845492 68 0 0 34.273428 39.753294 69 0 0 34.147501 39.654945 70 0 0 34.022581 39.556228 71 0 0 33.892 39.452028 72 0 0 33.748811 39.336547 73 0 0 33.627485 39.24053 74 0 0 33.502923 39.141328 75 0 0 33.390589 39.054062 76 0 0 33.288003 38.974148 77 0 0 33.191905 38.900038 78 0 0 33.104936 38.835632 79 0 0 33.012901 38.758399 80 0 0 32.9629 38.716955 81 0 0 32.906583 38.671211 82 0 0 32.871433 38.637745 83 0 0 32.845482 38.613817 84 0 0 32.816115 38.588633 85 0 0 32.785679 38.563387 86 0 0 32.753276 38.536493 87 0 0 32.730701 38.516463 88 0 0 32.688133 38.478458 89 0 0 32.645106 38.436687 90 0 0 32.598351 38.398072 91 0 0 32.565192 38.368843 92 0 0 32.523728 38.328187 93 0 0 32.488124 38.300526 94 0 0 32.461527 38.278039 95 0 0 32.425395 38.249123 96 0 0 32.41336 38.241182 97 0 0 32.403046 38.229534 98 0 0 32.39322 38.220008 99 0 0 32.413604 38.236321 100 0 0 32.458637 38.272346 101 0 0 32.500957 38.304792 102 0 0 32.553001 38.342992 103 0 0 32.591994 38.375267 104 0 0 32.633176 38.401094 105 0 0 32.662227 38.421163 106 0 0 32.691328 38.442099 107 0 0 32.704619 38.44809 108 0 0 32.713708 38.457779 109 0 0 32.717822 38.458825 110 0 0 32.708724 38.451982 111 0 0 32.676809 38.425052 112 0 0 32.65296 38.407284 113 0 0 32.592988 38.358622 114 0 0 32.556661 38.329777 115 0 0 32.527654 38.31058 116 0 0 32.501292 38.28621 117 0 0 32.496986 38.28653 118 0 0 32.473467 38.269187 119 0 0 32.491342 38.285672 120 0 0 32.512489 38.304219 121 0 0 32.529015 38.313057 122 0 0 32.552669 38.332018 123 0 0 32.576432 38.347221 124 0 0 32.59291 38.36139 125 0 0 32.607342 38.36861 126 0 0 32.62447 38.375099 127 0 0 32.633864 38.382408 128 0 0 32.631427 38.374272 129 0 0 32.618427 38.363389 130 0 0 32.599964 38.348158 131 0 0 32.591253 38.337753 132 0 0 32.588356 38.338242 133 0 0 32.585193 38.336112 134 0 0 32.555993 38.307719 135 0 0 32.554139 38.307252 136 0 0 32.546504 38.2978 137 0 0 32.544377 38.293833 138 0 0 32.560325 38.308894 139 0 0 32.542218 38.291175 140 0 0 32.59229 38.335786 141 0 0 32.625282 38.365983 142 0 0 32.641968 38.373756 143 0 0 32.647262 38.379668 144 0 0 32.665965 38.391896 145 0 0 32.630956 38.36488 146 0 0 32.601355 38.332105 147 0 0 32.586538 38.319822 148 0 0 32.544284 38.283083 149 0 0 32.528375 38.270126 150 0 0 32.490862 38.23947 151 0 0 32.47324 38.22481 152 0 0 32.448859 38.20447 153 0 0 32.418451 38.184833 154 0 0 32.428206 38.188811 155 0 0 32.427134 38.18698 156 0 0 32.450469 38.206835 157 0 0 32.447296 38.20095 158 0 0 32.468056 38.220991 159 0 0 32.541969 38.277735 160 0 0 32.524278 38.261057 161 0 0 32.580904 38.306574 162 0 0 32.631758 38.348407 163 0 0 32.612572 38.330233 164 0 0 32.630729 38.351827 165 0 0 32.636134 38.347315 166 0 0 32.655974 38.35155 167 0 0 32.642429 38.34228 168 0 0 32.597267 38.297779 169 0 0 32.567031 38.275381 170 0 0 32.543668 38.253423 171 0 0 32.478554 38.201969 172 0 0 32.494629 38.219767 173 0 0 32.513646 38.237321 174 0 0 32.534085 38.252354 175 0 0 32.572472 38.284392 176 0 0 32.560275 38.27162 177 0 0 32.569596 38.290342 178 0 0 32.633009 38.338941 179 0 0 32.69987 38.395546 180 0 0 32.754828 38.43994 181 0 0 32.794175 38.47647 182 0 0 32.805679 38.48818 183 0 0 32.857345 38.528777 184 0 0 32.88173 38.552658 185 0 0 32.926711 38.590538 186 0 0 32.976886 38.627882 187 0 0 32.98855 38.640019 188 0 0 33.04026 38.679339 189 0 0 33.022082 38.666049 190 0 0 32.996776 38.646665 191 0 0 32.992706 38.656056 192 0 0 32.968525 38.639468 193 0 0 32.914332 38.60197 194 0 0 32.953352 38.633486 195 0 0 32.939969 38.631773 196 0 0 32.906147 38.611287 197 0 0 32.910117 38.619389 198 0 0 32.880921 38.611403 199 0 0 32.875988 38.616394 200 0 0 32.894147 38.632136 201 0 0 32.874736 38.623657 202 0 0 32.8103 38.583316 203 0 0 32.785988 38.57458 204 0 0 32.827036 38.610584 205 0 0 32.813298 38.603372 206 0 0 32.774895 38.571459 207 0 0 32.760366 38.579105 208 0 0 32.728161 38.564168 209 0 0 32.710201 38.55237 210 0 0 32.664429 38.5029 211 0 0 32.699992 38.540523 212 0 0 32.5947 38.467838 213 0 0 32.625735 38.485733 214 0 0 32.54698 38.448156 215 0 0 32.59131 38.487086 216 0 0 32.532128 38.444881 217 0 0 32.558629 38.455938 218 0 0 32.514595 38.436078 219 0 0 32.50481 38.420559 220 0 0 32.495366 38.426485 221 0 0 32.485407 38.415454 222 0 0 32.499108 38.436571 223 0 0 32.485294 38.432097 224 0 0 32.43778 38.39375 225 0 0 32.428396 38.378988 226 0 0 32.360098 38.34929 227 0 0 32.346791 38.332034 228 0 0 32.30872 38.301797 229 0 0 32.286269 38.269744 230 0 0 32.244414 38.254479 231 0 0 32.337924 38.319395 232 0 0 32.347596 38.341162 233 0 0 32.298733 38.304409 234 0 0 32.153188 38.209533 235 0 0 32.246196 38.27131 236 0 0 32.278654 38.32425 237 0 0 32.112355 38.179768 238 0 0 32.131355 38.216036 239 0 0 32.132806 38.19216 240 0 0 32.06595 38.191737 241 0 0 32.032231 38.152008 242 0 0 32.014244 38.117528 243 0 0 31.98228 38.11641 244 0 0 31.87143 38.065374 245 0 0 31.857081 38.062648 246 0 0 31.849819 38.024198 247 0 0 32.00388 38.143977 248 0 0 31.796907 38.022688 249 0 0 31.849483 38.043864 250 0 0 31.873413 38.060566 251 0 0 31.801921 38.023226 252 0 0 31.653889 37.906361 253 0 0 31.621829 37.91564 254 0 0 31.413462 37.76237 255 0 0 31.551356 37.85985 256 0 0 31.551575 37.867584 257 0 0 31.350883 37.71607 258 0 0 31.422571 37.789824 259 0 0 31.405506 37.73231 260 0 0 31.39526 37.777636 261 0 0 31.377593 37.751477 262 0 0 31.250824 37.655739 263 0 0 31.287518 37.722701 264 0 0 31.251549 37.681192 265 0 0 31.263035 37.6949 266 0 0 31.172353 37.579761 267 0 0 30.971011 37.482472 268 0 0 30.807728 37.343683 269 0 0 31.092217 37.573742 270 0 0 31.039477 37.549447 271 0 0 30.979322 37.480485 272 0 0 30.637611 37.24515 273 0 0 30.752017 37.333594 274 0 0 30.502938 37.178775 275 0 0 30.497121 37.197331 276 0 0 30.327548 37.030608 277 0 0 30.285141 36.976286 278 0 0 30.444051 37.126661 279 0 0 30.370191 37.057558 280 0 0 30.078193 36.907165 281 0 0 30.228415 37.007839 282 0 0 30.163685 36.952618 283 0 0 30.005118 36.830092 284 0 0 30.033392 36.901699 285 0 0 29.554951 36.563656 286 0 0 29.748234 36.664683 287 0 0 30.074513 36.94039 288 0 0 29.644208 36.587733 289 0 0 29.438817 36.396948 290 0 0 29.412204 36.47198 291 0 0 29.357849 36.448746 292 0 0 29.168075 36.278198 293 0 0 29.050879 36.237126 294 0 0 28.912104 36.038585 295 0 0 28.7997 35.993824 296 0 0 28.787785 36.03951 297 0 0 28.949024 36.159255 298 0 0 29.119771 36.212416 299 0 0 28.786232 35.955515 300 0 0 29.107663 36.188727 301 0 0 28.520347 35.855904 302 0 0 28.919915 36.06095 303 0 0 28.873123 36.03028 304 0 0 28.448931 35.762998 305 0 0 28.373847 35.650182 306 0 0 28.626667 36.056 307 0 0 28.910816 35.983555 308 0 0 28.804281 36.007136 309 0 0 28.13067 35.443125 310 0 0 28.203872 35.6082 311 0 0 28.245721 35.634067 312 0 0 27.866755 35.220317 313 0 0 27.858571 35.341429 314 0 0 28.755832 36.007776 315 0 0 28.260135 35.566441 316 0 0 28.716636 35.932358 317 0 0 28.023857 35.551359 318 0 0 27.254274 34.719373 319 0 0 27.877315 35.416667 320 0 0 28.858561 35.972705 321 0 0 27.742466 35.445662 322 0 0 27.816568 35.147929 323 0 0 27.360927 34.821192 324 0 0 27.950943 35.561006 325 0 0 27.321586 35.142438 326 0 0 27.078431 34.785948 327 0 0 27.471204 34.965096 328 0 0 27.609195 34.881226 329 0 0 27.229814 34.757764 330 0 0 27.216783 35.032634 331 0 0 26.939394 34.623737 332 0 0 28.563025 35.963585 333 0 0 27.302083 34.548611 334 0 0 28.139535 35.996124 335 0 0 27.666667 35.466667 336 0 0 27.318841 34.444444 337 0 0 27.95 35.055556 338 0 0 27.836735 35.619048 339 0 0 27.619048 34.626984 340 0 0 29.27027 36.657658 341 0 0 27.035714 34.857143 342 0 0 26.32 35.12 343 0 0 26.863636 34.878788 344 0 0 28.842105 36.649123 345 0 0 29.166667 36.75 346 0 0 25.3 33.666667 347 0 0 25.8 33.166667 348 0 0 30.625 37.541667 349 0 0 29.125 36.041667 350 0 0 31.285714 37.47619 351 0 0 32.285714 38.190476 352 0 0 28.666667 34.444444 353 0 0 29.5 36.222222 354 0 0 31.666667 38.888889 355 0 0 31.8 38.466667 356 0 0 33.2 38.333333 357 0 0 35.75 40.5 358 0 0 26 36.083333 359 0 0 24.666667 35.555556 360 0 0 30.333333 36.666667 361 0 0 29 35.666667 362 0 0 24 33.166667 363 0 0 23 34.166667 364 0 0 32.5 38.666667 365 0 0 28.5 37 366 0 0 22 28.166667 367 0 0 25.5 36.166667 368 0 0 15.5 28.666667 369 0 0 23 35