## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5388-Z0074-CTATGAATGAGCGAT/441525-L5388-Z0074-CTATGAATGAGCGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5388-Z0074-CTATGAATGAGCGAT/441525-L5388-Z0074-CTATGAATGAGCGAT_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 02:56:37 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 999825 999825 132 132016299 132016299 127100924 127100924 117975107 117975107 0 0 0.962767 0.89364 0 0.962767 0.89364 0 396048897 396048897 389525413 389525413 374896568 374896568 350421342 350421342 0.983529 0.946592 0.884793 0.983529 0.946592 0.884793 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 853 0 35.994971 40.996102 1 10894 0 35.98898 40.992207 2 13358 4259 35.995327 40.996008 3 33729 1270 35.984799 40.987685 4 55576 47206 35.992243 40.993613 5 109773 18244 35.995886 40.996581 6 111232 121997 35.978821 40.982618 7 193926 157218 35.978743 40.985348 8 197323 149560 35.98911 40.990952 9 241612 109464 35.966157 40.971511 10 252390 509122 35.863086 40.922526 11 297963 61565 35.907655 40.930018 12 357081 710509 35.160281 40.288783 13 353381 208808 33.487772 39.445077 14 464347 1001730 35.877727 40.92462 15 374201 381660 35.835016 40.883143 16 389519 449662 35.807875 40.828611 17 523395 1132173 35.906963 40.921417 18 559381 746253 35.734305 40.779911 19 375441 712784 35.741694 40.809415 20 507334 1008651 35.903234 40.936118 21 673969 1394516 35.825404 40.873128 22 319594 560664 35.591465 40.723252 23 1022964 1198415 35.286505 40.510491 24 582998 1193918 35.297453 40.525264 25 541407 474689 35.309567 40.534511 26 1733341 2490687 35.24414 40.479295 27 358124 852143 35.264361 40.499097 28 951865 389417 35.275782 40.508941 29 2434221 5065745 35.275556 40.506464 30 754577 40457 35.278213 40.508312 31 2315750 795544 35.272177 40.502623 32 1599599 5437771 35.267195 40.495603 33 839564 123101 35.27128 40.50291 34 2430541 2632955 35.266351 40.499066 35 2183536 3805406 35.280635 40.509172 36 107851540 2096726 35.309967 40.528886 37 0 4227579 35.316821 40.534894 38 0 364360 35.299826 40.524299 39 0 4951327 35.299285 40.523669 40 0 0 35.298983 40.521171 41 0 350421342 35.282402 40.51048 42 0 0 35.277753 40.505211 43 0 0 35.280675 40.508335 44 0 0 35.290278 40.515797 45 0 0 35.296376 40.519739 46 0 0 35.2836 40.510708 47 0 0 35.276066 40.504687 48 0 0 35.263538 40.496408 49 0 0 35.258003 40.491659 50 0 0 35.261553 40.492973 51 0 0 35.248181 40.485116 52 0 0 35.234704 40.477084 53 0 0 35.214782 40.466857 54 0 0 35.212445 40.462264 55 0 0 35.205785 40.457331 56 0 0 35.177715 40.440714 57 0 0 35.179184 40.43807 58 0 0 35.152074 40.417551 59 0 0 35.136536 40.404734 60 0 0 35.101782 40.379961 61 0 0 35.065554 40.352644 62 0 0 35.026142 40.323742 63 0 0 34.981838 40.289134 64 0 0 34.928696 40.250693 65 0 0 34.883643 40.218595 66 0 0 34.815989 40.168337 67 0 0 34.750481 40.118915 68 0 0 34.675533 40.065389 69 0 0 34.596806 40.003492 70 0 0 34.509394 39.935943 71 0 0 34.411857 39.858375 72 0 0 34.313479 39.78152 73 0 0 34.2094 39.697665 74 0 0 34.106901 39.614938 75 0 0 33.999516 39.532647 76 0 0 33.880066 39.441381 77 0 0 33.787236 39.370741 78 0 0 33.695039 39.300232 79 0 0 33.599727 39.223989 80 0 0 33.504699 39.147285 81 0 0 33.421044 39.08066 82 0 0 33.339484 39.012701 83 0 0 33.267038 38.956636 84 0 0 33.206181 38.907499 85 0 0 33.147132 38.860883 86 0 0 33.093748 38.816627 87 0 0 33.032719 38.766376 88 0 0 32.976555 38.719471 89 0 0 32.910195 38.662203 90 0 0 32.863197 38.62443 91 0 0 32.800033 38.568043 92 0 0 32.758588 38.530015 93 0 0 32.726491 38.500517 94 0 0 32.686639 38.469682 95 0 0 32.654844 38.439825 96 0 0 32.639256 38.426702 97 0 0 32.619115 38.409528 98 0 0 32.608301 38.399967 99 0 0 32.642285 38.425086 100 0 0 32.649149 38.431754 101 0 0 32.693357 38.465215 102 0 0 32.723361 38.488147 103 0 0 32.768362 38.520683 104 0 0 32.769561 38.517323 105 0 0 32.792773 38.534632 106 0 0 32.810581 38.54175 107 0 0 32.79413 38.528133 108 0 0 32.788004 38.521297 109 0 0 32.767389 38.508409 110 0 0 32.722571 38.475076 111 0 0 32.688546 38.445654 112 0 0 32.646635 38.407954 113 0 0 32.579317 38.352993 114 0 0 32.518474 38.305126 115 0 0 32.466968 38.262665 116 0 0 32.440103 38.241928 117 0 0 32.40798 38.218136 118 0 0 32.394388 38.21466 119 0 0 32.403873 38.21891 120 0 0 32.410183 38.224696 121 0 0 32.417028 38.232113 122 0 0 32.424547 38.232114 123 0 0 32.450535 38.254174 124 0 0 32.458728 38.256407 125 0 0 32.461126 38.254876 126 0 0 32.487986 38.271904 127 0 0 32.490108 38.270059 128 0 0 32.465083 38.241786 129 0 0 32.43713 38.222831 130 0 0 32.401107 38.193046 131 0 0 32.390859 38.1816 132 0 0 32.375611 38.164126 133 0 0 32.360788 38.15681 134 0 0 32.364588 38.156166 135 0 0 32.363814 38.150671 136 0 0 32.349304 38.137713 137 0 0 32.352002 38.142609 138 0 0 32.338471 38.133872 139 0 0 32.389848 38.174689 140 0 0 32.40942 38.186558 141 0 0 32.43705 38.213901 142 0 0 32.458511 38.230563 143 0 0 32.45295 38.227679 144 0 0 32.476013 38.239092 145 0 0 32.445829 38.218106 146 0 0 32.424573 38.192579 147 0 0 32.40171 38.174069 148 0 0 32.367807 38.13808 149 0 0 32.319856 38.104362 150 0 0 32.29936 38.083717 151 0 0 32.258357 38.053119 152 0 0 32.259843 38.057907 153 0 0 32.248248 38.04917 154 0 0 32.216157 38.020801 155 0 0 32.243584 38.046482 156 0 0 32.254625 38.053336 157 0 0 32.284652 38.073157 158 0 0 32.32271 38.101793 159 0 0 32.356133 38.130373 160 0 0 32.406537 38.167874 161 0 0 32.439808 38.199753 162 0 0 32.490018 38.238409 163 0 0 32.509316 38.247911 164 0 0 32.552024 38.286789 165 0 0 32.55843 38.28728 166 0 0 32.554561 38.279746 167 0 0 32.543086 38.272271 168 0 0 32.522423 38.247719 169 0 0 32.457595 38.190509 170 0 0 32.460364 38.194591 171 0 0 32.428425 38.176514 172 0 0 32.411306 38.158751 173 0 0 32.454632 38.204972 174 0 0 32.415311 38.167305 175 0 0 32.472424 38.2173 176 0 0 32.517781 38.252577 177 0 0 32.567395 38.295653 178 0 0 32.61053 38.327475 179 0 0 32.656685 38.371655 180 0 0 32.737089 38.445421 181 0 0 32.782718 38.480944 182 0 0 32.819448 38.51278 183 0 0 32.857117 38.541449 184 0 0 32.89927 38.569487 185 0 0 32.895592 38.574766 186 0 0 32.965766 38.632957 187 0 0 32.982733 38.650988 188 0 0 33.006131 38.664534 189 0 0 33.021888 38.674684 190 0 0 33.0119 38.676396 191 0 0 32.997499 38.666813 192 0 0 32.965509 38.648333 193 0 0 32.931071 38.624177 194 0 0 32.969003 38.664435 195 0 0 32.886443 38.606594 196 0 0 32.949615 38.653758 197 0 0 32.916434 38.635538 198 0 0 32.892857 38.622396 199 0 0 32.941995 38.662251 200 0 0 32.857084 38.610391 201 0 0 32.843067 38.612052 202 0 0 32.891474 38.658283 203 0 0 32.847394 38.631255 204 0 0 32.875101 38.658917 205 0 0 32.818878 38.619911 206 0 0 32.810283 38.628032 207 0 0 32.876876 38.680623 208 0 0 32.735519 38.57917 209 0 0 32.749247 38.576657 210 0 0 32.758305 38.603417 211 0 0 32.689854 38.554847 212 0 0 32.657272 38.516415 213 0 0 32.686859 38.559187 214 0 0 32.707477 38.585367 215 0 0 32.697323 38.556663 216 0 0 32.655689 38.547644 217 0 0 32.604729 38.512642 218 0 0 32.565285 38.47683 219 0 0 32.595166 38.50841 220 0 0 32.55498 38.470365 221 0 0 32.50675 38.443569 222 0 0 32.570059 38.486986 223 0 0 32.504991 38.440589 224 0 0 32.434945 38.406225 225 0 0 32.360654 38.348518 226 0 0 32.409041 38.394261 227 0 0 32.450278 38.417663 228 0 0 32.382076 38.369144 229 0 0 32.337931 38.350208 230 0 0 32.358395 38.366393 231 0 0 32.429048 38.397981 232 0 0 32.344185 38.347208 233 0 0 32.302032 38.330367 234 0 0 32.306744 38.341373 235 0 0 32.294126 38.312415 236 0 0 32.180842 38.238697 237 0 0 32.195526 38.258648 238 0 0 32.1493 38.226219 239 0 0 32.33336 38.364481 240 0 0 32.075564 38.170347 241 0 0 32.14172 38.223868 242 0 0 32.175204 38.26066 243 0 0 32.122731 38.197954 244 0 0 32.032282 38.165259 245 0 0 31.793003 38.031066 246 0 0 31.941171 38.104731 247 0 0 31.875653 38.075479 248 0 0 31.899137 38.073319 249 0 0 31.958961 38.134716 250 0 0 31.833429 38.021703 251 0 0 32.021874 38.157275 252 0 0 31.888629 38.06858 253 0 0 31.842125 38.082781 254 0 0 31.736011 37.94097 255 0 0 31.682609 37.931476 256 0 0 31.796216 38.04646 257 0 0 31.743115 37.978294 258 0 0 31.689269 37.930228 259 0 0 31.521185 37.833662 260 0 0 31.497346 37.807993 261 0 0 31.56249 37.854163 262 0 0 31.299109 37.709585 263 0 0 31.620942 37.94249 264 0 0 31.405918 37.768262 265 0 0 31.274629 37.66166 266 0 0 31.214797 37.649715 267 0 0 31.337665 37.74752 268 0 0 31.21314 37.665443 269 0 0 31.075509 37.603808 270 0 0 30.934642 37.456158 271 0 0 30.918655 37.429273 272 0 0 30.845453 37.384849 273 0 0 30.797967 37.403634 274 0 0 30.704661 37.285104 275 0 0 30.679682 37.31154 276 0 0 30.686429 37.299907 277 0 0 30.669435 37.352713 278 0 0 30.480755 37.135318 279 0 0 30.352461 37.075109 280 0 0 30.381025 37.09124 281 0 0 30.257921 36.956795 282 0 0 30.200592 36.944161 283 0 0 29.91214 36.765706 284 0 0 29.962232 36.81774 285 0 0 29.803356 36.725542 286 0 0 29.633546 36.605287 287 0 0 29.821507 36.719857 288 0 0 29.804184 36.675057 289 0 0 29.53252 36.515357 290 0 0 29.678697 36.607568 291 0 0 29.578182 36.568242 292 0 0 29.344711 36.332833 293 0 0 29.600626 36.624772 294 0 0 29.270049 36.347109 295 0 0 29.452694 36.480696 296 0 0 29.258476 36.348451 297 0 0 28.997701 36.130575 298 0 0 29.332046 36.382239 299 0 0 29.10441 36.281298 300 0 0 28.973433 36.162593 301 0 0 29.071669 36.219485 302 0 0 29.025989 36.146289 303 0 0 28.718092 35.9019 304 0 0 28.773535 35.942506 305 0 0 28.897275 36.060564 306 0 0 28.852919 36.00813 307 0 0 28.737421 35.902254 308 0 0 28.459504 35.727273 309 0 0 28.676208 35.831843 310 0 0 28.284342 35.574448 311 0 0 28.746625 35.959848 312 0 0 28.970819 36.028807 313 0 0 28.793269 36.002804 314 0 0 28.134211 35.633772 315 0 0 28.164502 35.530063 316 0 0 28.15625 35.676042 317 0 0 28.174957 35.595769 318 0 0 27.965909 35.328283 319 0 0 27.828866 35.18488 320 0 0 28.362416 35.685309 321 0 0 28.660287 35.916268 322 0 0 27.198966 34.768303 323 0 0 28.293296 35.671322 324 0 0 27.763578 35.388711 325 0 0 27.870968 35.493429 326 0 0 27.943089 35.531165 327 0 0 27.506726 35.164425 328 0 0 28.417476 35.920712 329 0 0 27.883598 35.416226 330 0 0 27.393939 35.105051 331 0 0 28.536424 35.690949 332 0 0 26.963235 34.539216 333 0 0 27.672269 35.473389 334 0 0 26.46729 34.563863 335 0 0 27.515789 35.077193 336 0 0 27.493976 35.554217 337 0 0 27 35.455399 338 0 0 28.459016 36.169399 339 0 0 25.655172 33.5 340 0 0 26.3125 34.631944 341 0 0 28.186047 35.20155 342 0 0 28.25 35.7 343 0 0 26.157895 34.201754 344 0 0 26.333333 34.138889 345 0 0 28.6 36 346 0 0 25.892857 34.380952 347 0 0 25.923077 34 348 0 0 25.26087 33.434783 349 0 0 28.111111 35.148148 350 0 0 24 32.577778 351 0 0 29.5 36.928571 352 0 0 25.333333 33.333333 353 0 0 23.5 33.277778 354 0 0 28 35.5 355 0 0 28.333333 36.333333 356 0 0 21.666667 29.111111 357 0 0 36 41 358 0 0 9 30.333333 359 0 0 24 35.333333 360 0 0 36 41 361 0 0 36 41 362 0 0 23 31 363 0 0 19 28.333333 364 0 0 7 16.333333 365 0 0 32 38 366 0 0 26 36