## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5272-Z0011-CACGCACTGCCAGAT/441525-L5272-Z0011-CACGCACTGCCAGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5272-Z0011-CACGCACTGCCAGAT/441525-L5272-Z0011-CACGCACTGCCAGAT_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 02:56:44 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 1001158 1001158 142 142990083 142990083 138019280 138019280 128410990 128410990 0 0 0.965237 0.898041 0 0.965237 0.898041 0 428970249 428970249 422447542 422447542 407106286 407106286 381155581 381155581 0.984795 0.949032 0.888536 0.984795 0.949032 0.888536 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 890 0 35.981551 40.987338 1 12055 0 35.970948 40.980418 2 14830 5172 35.985181 40.988265 3 36832 1343 35.868863 40.899333 4 57867 51106 35.95311 40.962594 5 117613 17394 35.966104 40.973596 6 110198 134502 35.913875 40.934171 7 204177 167328 35.946891 40.963672 8 192235 152035 35.963881 40.972167 9 244839 113075 35.923395 40.937094 10 254941 517349 35.858936 40.908435 11 301028 64442 35.90459 40.930765 12 350789 716149 35.324791 40.441244 13 355340 205666 34.048659 39.797263 14 463163 993638 35.857578 40.913219 15 382425 381785 35.794025 40.854037 16 385560 432818 35.751114 40.780598 17 531408 1110216 35.887075 40.906016 18 562878 751000 35.69338 40.746111 19 391735 707689 35.742291 40.803428 20 540756 1023756 35.906979 40.935753 21 684145 1427707 35.834639 40.881215 22 346797 565571 35.603652 40.730401 23 1106829 1313743 35.304068 40.533113 24 608963 1254095 35.310653 40.53517 25 565448 507210 35.303666 40.526752 26 1838940 2637529 35.256958 40.491552 27 381173 948434 35.271293 40.507606 28 987554 416708 35.291981 40.522394 29 2547685 5246503 35.283252 40.515092 30 821082 41982 35.27157 40.506887 31 2495703 910223 35.266761 40.501245 32 1726129 5588072 35.262823 40.497935 33 900450 130961 35.261835 40.49865 34 2603192 2876666 35.253813 40.493031 35 2361416 3978068 35.271946 40.50589 36 117503018 2258935 35.293688 40.52006 37 0 4431552 35.294907 40.523324 38 0 431577 35.286033 40.518049 39 0 5302669 35.291428 40.521801 40 0 6 35.279113 40.512452 41 0 381155575 35.268528 40.503328 42 0 0 35.256399 40.495419 43 0 0 35.267024 40.502221 44 0 0 35.277095 40.508396 45 0 0 35.277936 40.510101 46 0 0 35.27935 40.510983 47 0 0 35.27153 40.50561 48 0 0 35.263196 40.499631 49 0 0 35.264565 40.500427 50 0 0 35.25882 40.495681 51 0 0 35.249947 40.490081 52 0 0 35.240327 40.482724 53 0 0 35.226532 40.474857 54 0 0 35.225196 40.473031 55 0 0 35.212853 40.463894 56 0 0 35.187498 40.447573 57 0 0 35.178156 40.439704 58 0 0 35.159568 40.425371 59 0 0 35.126391 40.40179 60 0 0 35.09629 40.378082 61 0 0 35.044224 40.339406 62 0 0 34.993403 40.299429 63 0 0 34.938694 40.257072 64 0 0 34.880757 40.211593 65 0 0 34.809171 40.157353 66 0 0 34.737045 40.104371 67 0 0 34.643248 40.034055 68 0 0 34.555887 39.969517 69 0 0 34.454725 39.889676 70 0 0 34.360139 39.811051 71 0 0 34.247885 39.724459 72 0 0 34.15112 39.644645 73 0 0 34.042004 39.557341 74 0 0 33.952389 39.486923 75 0 0 33.865961 39.419226 76 0 0 33.776365 39.350917 77 0 0 33.707461 39.297699 78 0 0 33.650536 39.253383 79 0 0 33.59828 39.212743 80 0 0 33.553915 39.17336 81 0 0 33.522215 39.147411 82 0 0 33.478474 39.11159 83 0 0 33.457596 39.08989 84 0 0 33.436921 39.072415 85 0 0 33.427354 39.064367 86 0 0 33.404023 39.043154 87 0 0 33.374441 39.016291 88 0 0 33.348126 38.99373 89 0 0 33.304771 38.954446 90 0 0 33.26121 38.918176 91 0 0 33.230512 38.891236 92 0 0 33.203122 38.864908 93 0 0 33.176812 38.843445 94 0 0 33.137875 38.809857 95 0 0 33.11302 38.791892 96 0 0 33.092828 38.773267 97 0 0 33.093035 38.772825 98 0 0 33.108075 38.784252 99 0 0 33.117398 38.792073 100 0 0 33.156912 38.825269 101 0 0 33.204124 38.862612 102 0 0 33.241979 38.889616 103 0 0 33.276053 38.914266 104 0 0 33.304267 38.935488 105 0 0 33.322833 38.947049 106 0 0 33.331205 38.950575 107 0 0 33.33764 38.953422 108 0 0 33.331648 38.948153 109 0 0 33.317104 38.937365 110 0 0 33.293046 38.917717 111 0 0 33.256851 38.889975 112 0 0 33.212946 38.853542 113 0 0 33.164835 38.817058 114 0 0 33.124043 38.779046 115 0 0 33.082174 38.745611 116 0 0 33.044336 38.712945 117 0 0 33.042645 38.715789 118 0 0 33.027675 38.708489 119 0 0 33.047128 38.725018 120 0 0 33.043867 38.726546 121 0 0 33.064608 38.741843 122 0 0 33.085082 38.757665 123 0 0 33.09982 38.764681 124 0 0 33.103257 38.763861 125 0 0 33.117876 38.774975 126 0 0 33.128843 38.775767 127 0 0 33.128214 38.772293 128 0 0 33.119352 38.764132 129 0 0 33.086629 38.734243 130 0 0 33.071198 38.723827 131 0 0 33.044711 38.699223 132 0 0 33.04244 38.698805 133 0 0 33.030157 38.687431 134 0 0 33.026902 38.681597 135 0 0 33.034311 38.688511 136 0 0 33.015787 38.674246 137 0 0 33.022481 38.674733 138 0 0 33.029788 38.684216 139 0 0 33.050069 38.698464 140 0 0 33.067977 38.716968 141 0 0 33.080872 38.73012 142 0 0 33.096488 38.742076 143 0 0 33.110504 38.749046 144 0 0 33.082859 38.727209 145 0 0 33.073384 38.715371 146 0 0 33.055525 38.694452 147 0 0 33.01497 38.66633 148 0 0 32.970905 38.6288 149 0 0 32.940831 38.600463 150 0 0 32.916629 38.582103 151 0 0 32.88909 38.560555 152 0 0 32.874734 38.553763 153 0 0 32.884885 38.559734 154 0 0 32.887405 38.560415 155 0 0 32.879959 38.557754 156 0 0 32.87808 38.549168 157 0 0 32.930689 38.593112 158 0 0 32.940907 38.60317 159 0 0 32.960986 38.614948 160 0 0 33.024455 38.668028 161 0 0 33.044275 38.681467 162 0 0 33.074964 38.705211 163 0 0 33.099869 38.728842 164 0 0 33.121457 38.740542 165 0 0 33.113847 38.73429 166 0 0 33.115074 38.736822 167 0 0 33.082598 38.703824 168 0 0 33.061524 38.685017 169 0 0 33.017932 38.648025 170 0 0 32.990441 38.623771 171 0 0 32.983006 38.619928 172 0 0 32.96441 38.606781 173 0 0 33.002992 38.642944 174 0 0 32.999048 38.638111 175 0 0 33.003485 38.643601 176 0 0 33.033975 38.671581 177 0 0 33.071918 38.706825 178 0 0 33.098453 38.718171 179 0 0 33.133017 38.756476 180 0 0 33.151172 38.767742 181 0 0 33.222965 38.8329 182 0 0 33.2468 38.851078 183 0 0 33.285793 38.882636 184 0 0 33.326229 38.914046 185 0 0 33.356525 38.940295 186 0 0 33.386577 38.963576 187 0 0 33.415926 38.986623 188 0 0 33.422713 38.991518 189 0 0 33.41649 38.995905 190 0 0 33.412243 38.992589 191 0 0 33.426425 39.001674 192 0 0 33.367469 38.96244 193 0 0 33.345853 38.950197 194 0 0 33.310883 38.925274 195 0 0 33.331656 38.946387 196 0 0 33.329315 38.954445 197 0 0 33.310654 38.940013 198 0 0 33.338031 38.964181 199 0 0 33.318609 38.963116 200 0 0 33.323833 38.96431 201 0 0 33.308626 38.964397 202 0 0 33.308361 38.970963 203 0 0 33.268843 38.946896 204 0 0 33.249836 38.937138 205 0 0 33.239915 38.933697 206 0 0 33.237324 38.937168 207 0 0 33.192386 38.909411 208 0 0 33.20041 38.91547 209 0 0 33.183599 38.907432 210 0 0 33.157769 38.886081 211 0 0 33.162148 38.900446 212 0 0 33.120948 38.879244 213 0 0 33.118671 38.873911 214 0 0 33.092916 38.861138 215 0 0 33.032948 38.830565 216 0 0 33.038841 38.831135 217 0 0 33.044737 38.830843 218 0 0 32.994453 38.80136 219 0 0 32.962567 38.773904 220 0 0 32.954008 38.770773 221 0 0 32.918057 38.75219 222 0 0 32.918899 38.751744 223 0 0 32.886757 38.738468 224 0 0 32.831816 38.69645 225 0 0 32.83509 38.694487 226 0 0 32.81442 38.689847 227 0 0 32.795047 38.667997 228 0 0 32.733832 38.630338 229 0 0 32.722671 38.626188 230 0 0 32.697044 38.610096 231 0 0 32.671255 38.594503 232 0 0 32.65788 38.585059 233 0 0 32.700925 38.623243 234 0 0 32.679086 38.60601 235 0 0 32.620172 38.569096 236 0 0 32.626794 38.574833 237 0 0 32.584822 38.546409 238 0 0 32.538899 38.527914 239 0 0 32.513391 38.494132 240 0 0 32.482113 38.469066 241 0 0 32.482564 38.468873 242 0 0 32.398152 38.42641 243 0 0 32.366256 38.401867 244 0 0 32.377512 38.423204 245 0 0 32.291225 38.372832 246 0 0 32.282075 38.338048 247 0 0 32.269735 38.329024 248 0 0 32.20554 38.301371 249 0 0 32.189181 38.289696 250 0 0 32.107419 38.227607 251 0 0 32.117732 38.263975 252 0 0 32.081402 38.229312 253 0 0 32.024424 38.198503 254 0 0 32.044201 38.187781 255 0 0 31.986357 38.163272 256 0 0 31.983674 38.154558 257 0 0 31.962032 38.152197 258 0 0 31.934414 38.13898 259 0 0 31.839808 38.065175 260 0 0 31.829394 38.05987 261 0 0 31.767512 38.012749 262 0 0 31.69587 37.982246 263 0 0 31.666529 37.972034 264 0 0 31.569534 37.894904 265 0 0 31.610656 37.917582 266 0 0 31.538047 37.885622 267 0 0 31.413227 37.807427 268 0 0 31.286685 37.704118 269 0 0 31.219606 37.669497 270 0 0 31.256752 37.696556 271 0 0 31.308254 37.751275 272 0 0 31.236852 37.685188 273 0 0 31.020705 37.542045 274 0 0 31.028684 37.56831 275 0 0 30.980215 37.516245 276 0 0 30.885115 37.445744 277 0 0 30.822597 37.399766 278 0 0 30.894413 37.471817 279 0 0 30.648491 37.275941 280 0 0 30.529894 37.210003 281 0 0 30.567043 37.23573 282 0 0 30.481223 37.169514 283 0 0 30.472428 37.161885 284 0 0 30.375467 37.106268 285 0 0 30.287702 37.039886 286 0 0 30.276079 37.040146 287 0 0 30.132821 36.973451 288 0 0 30.09064 36.896425 289 0 0 30.014301 36.852117 290 0 0 30.025232 36.882492 291 0 0 29.858869 36.760781 292 0 0 29.723986 36.658426 293 0 0 29.793209 36.705627 294 0 0 29.532823 36.481375 295 0 0 29.563887 36.543773 296 0 0 29.694541 36.635545 297 0 0 29.302885 36.41453 298 0 0 29.421085 36.440624 299 0 0 29.28123 36.402387 300 0 0 29.030415 36.168837 301 0 0 29.22187 36.358637 302 0 0 29.042174 36.167097 303 0 0 28.97252 36.081022 304 0 0 28.919951 36.104971 305 0 0 28.997715 36.156955 306 0 0 28.838973 35.993555 307 0 0 28.787971 35.964555 308 0 0 28.676425 35.88187 309 0 0 28.772628 35.985157 310 0 0 28.712615 35.975824 311 0 0 28.594182 35.913283 312 0 0 28.472322 35.776853 313 0 0 28.201875 35.609629 314 0 0 28.477244 35.827548 315 0 0 28.201172 35.583519 316 0 0 28.361471 35.748066 317 0 0 28.195988 35.527129 318 0 0 28.516338 35.814363 319 0 0 28.046659 35.488731 320 0 0 28.099569 35.543822 321 0 0 28.655221 35.861869 322 0 0 27.965517 35.359067 323 0 0 27.938901 35.37145 324 0 0 27.983136 35.421195 325 0 0 28.06694 35.517077 326 0 0 28.009752 35.487372 327 0 0 28.140704 35.559464 328 0 0 28.283161 35.619944 329 0 0 28.211518 35.626178 330 0 0 28.07783 35.449292 331 0 0 28.11008 35.414677 332 0 0 27.800287 35.327586 333 0 0 28.887836 36.058978 334 0 0 28.586022 35.839904 335 0 0 27.015968 34.578842 336 0 0 28.109375 35.456101 337 0 0 28.956853 36.016074 338 0 0 27.851632 35.330366 339 0 0 28.336667 35.613333 340 0 0 28.629771 36.109415 341 0 0 26.789954 34.780822 342 0 0 28.032086 35.424242 343 0 0 29.462963 36.611111 344 0 0 27.740458 35.328244 345 0 0 27.074766 35.099688 346 0 0 28.919192 35.649832 347 0 0 27.917647 35.486275 348 0 0 28.479452 35.689498 349 0 0 29.031746 36.10582 350 0 0 29.944444 37.049383 351 0 0 27.604651 35.418605 352 0 0 28.805556 36.425926 353 0 0 28.625 35.625 354 0 0 27.851852 35.259259 355 0 0 26.347826 34.028986 356 0 0 26.857143 34.492063 357 0 0 26.315789 34.578947 358 0 0 26.944444 34.555556 359 0 0 29.714286 37.238095 360 0 0 28 36.757576 361 0 0 25.375 33.833333 362 0 0 28.428571 35.52381 363 0 0 33 38.666667 364 0 0 29 34.857143 365 0 0 27.166667 34.277778 366 0 0 29.6 36 367 0 0 35 40.4 368 0 0 24.75 34.083333 369 0 0 31.25 37.75 370 0 0 27.5 34 371 0 0 32 37.583333 372 0 0 32.5 38.416667 373 0 0 36 41 374 0 0 31 36.5 375 0 0 20.5 30 376 0 0 25 34 377 0 0 36 41