## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5414-Z0109-CAATCTGCATACGAT/441525-L5414-Z0109-CAATCTGCATACGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5414-Z0109-CAATCTGCATACGAT/441525-L5414-Z0109-CAATCTGCATACGAT_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 02:56:41 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 999035 999035 130 130461022 130461022 125398622 125398622 116017418 116017418 0 0 0.961196 0.889288 0 0.961196 0.889288 0 391383066 391383066 384702589 384702589 369600779 369600779 344462251 344462251 0.982931 0.944345 0.880115 0.982931 0.944345 0.880115 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 942 0 35.995159 40.996332 1 12577 0 35.988648 40.992222 2 14597 4846 35.995364 40.996076 3 37734 1375 35.980131 40.983877 4 59326 53558 35.991039 40.992645 5 120997 18841 35.994929 40.995827 6 114446 137310 35.975416 40.97929 7 209302 170155 35.9725 40.981904 8 197461 157081 35.984632 40.987197 9 251494 120629 35.95409 40.960853 10 262976 528079 35.824862 40.89834 11 308520 68311 35.882479 40.911416 12 364380 731625 35.097791 40.244691 13 359454 214973 33.425709 39.412707 14 475363 1019473 35.844982 40.901411 15 385711 391142 35.854024 40.898366 16 392519 445506 35.838865 40.860108 17 536693 1129944 35.909243 40.924744 18 568987 768146 35.662236 40.717987 19 388921 719483 35.672129 40.75371 20 530423 1019613 35.881571 40.920491 21 691673 1432884 35.810482 40.863108 22 339088 568057 35.560217 40.697227 23 1070664 1263624 35.210885 40.452346 24 604947 1247227 35.214044 40.463648 25 555738 493298 35.225363 40.47538 26 1774368 2596145 35.149435 40.415818 27 377849 904603 35.174606 40.439989 28 970643 417260 35.190918 40.451148 29 2465811 5159099 35.189216 40.44889 30 781678 41694 35.185325 40.44645 31 2363329 859109 35.177618 40.438556 32 1686604 5489744 35.166084 40.427825 33 863791 133748 35.167859 40.432964 34 2493080 2788331 35.167413 40.431316 35 2221390 3859786 35.181934 40.441479 36 105607546 2223064 35.206106 40.45831 37 0 4276613 35.211196 40.46292 38 0 384825 35.201496 40.457194 39 0 5081614 35.195015 40.451221 40 0 1 35.18907 40.446169 41 0 344462250 35.170959 40.433336 42 0 0 35.165137 40.429042 43 0 0 35.172393 40.435624 44 0 0 35.178113 40.438481 45 0 0 35.185993 40.443276 46 0 0 35.16902 40.431633 47 0 0 35.162437 40.426412 48 0 0 35.152363 40.418636 49 0 0 35.1384 40.409699 50 0 0 35.139147 40.410722 51 0 0 35.139888 40.410239 52 0 0 35.106747 40.38694 53 0 0 35.091683 40.378669 54 0 0 35.087554 40.373342 55 0 0 35.064971 40.357351 56 0 0 35.039587 40.341617 57 0 0 35.055337 40.350806 58 0 0 35.029651 40.329021 59 0 0 35.003709 40.311165 60 0 0 34.973966 40.294123 61 0 0 34.9347 40.262929 62 0 0 34.909742 40.242313 63 0 0 34.860709 40.207438 64 0 0 34.807544 40.166469 65 0 0 34.756108 40.13012 66 0 0 34.702298 40.090101 67 0 0 34.638947 40.044105 68 0 0 34.561888 39.985466 69 0 0 34.484427 39.926361 70 0 0 34.385245 39.85093 71 0 0 34.281411 39.765988 72 0 0 34.167668 39.675564 73 0 0 34.053944 39.582623 74 0 0 33.939146 39.490459 75 0 0 33.826458 39.40133 76 0 0 33.701362 39.305986 77 0 0 33.59197 39.222581 78 0 0 33.477804 39.134194 79 0 0 33.37696 39.056077 80 0 0 33.283349 38.981448 81 0 0 33.18502 38.900735 82 0 0 33.115381 38.842397 83 0 0 33.035888 38.779487 84 0 0 32.981357 38.730874 85 0 0 32.916893 38.679706 86 0 0 32.861677 38.632515 87 0 0 32.807281 38.589572 88 0 0 32.742421 38.535493 89 0 0 32.683059 38.48373 90 0 0 32.638333 38.442649 91 0 0 32.586851 38.396751 92 0 0 32.542203 38.358189 93 0 0 32.506465 38.32751 94 0 0 32.480554 38.302658 95 0 0 32.46376 38.286922 96 0 0 32.446396 38.268572 97 0 0 32.42782 38.256392 98 0 0 32.435978 38.261523 99 0 0 32.478385 38.290322 100 0 0 32.509777 38.315791 101 0 0 32.546575 38.345588 102 0 0 32.593376 38.380483 103 0 0 32.63605 38.414189 104 0 0 32.658434 38.427334 105 0 0 32.671497 38.43593 106 0 0 32.670701 38.428543 107 0 0 32.666585 38.424141 108 0 0 32.656778 38.414605 109 0 0 32.623344 38.38766 110 0 0 32.589882 38.363528 111 0 0 32.552944 38.335316 112 0 0 32.488147 38.281229 113 0 0 32.436382 38.237566 114 0 0 32.384221 38.198392 115 0 0 32.309279 38.136707 116 0 0 32.281479 38.115327 117 0 0 32.260388 38.101997 118 0 0 32.267253 38.110766 119 0 0 32.280395 38.122063 120 0 0 32.299012 38.140552 121 0 0 32.343846 38.175445 122 0 0 32.352215 38.177271 123 0 0 32.38068 38.199814 124 0 0 32.420939 38.229217 125 0 0 32.400829 38.206735 126 0 0 32.423035 38.219728 127 0 0 32.438328 38.231461 128 0 0 32.444675 38.227592 129 0 0 32.425781 38.209769 130 0 0 32.398243 38.184751 131 0 0 32.370231 38.169846 132 0 0 32.376691 38.173059 133 0 0 32.377577 38.171279 134 0 0 32.382474 38.172629 135 0 0 32.373374 38.164268 136 0 0 32.37711 38.164354 137 0 0 32.370527 38.158863 138 0 0 32.371015 38.159904 139 0 0 32.407684 38.190149 140 0 0 32.425319 38.210753 141 0 0 32.469961 38.249377 142 0 0 32.499272 38.270679 143 0 0 32.506217 38.271809 144 0 0 32.492244 38.263433 145 0 0 32.491884 38.255691 146 0 0 32.480502 38.244867 147 0 0 32.445727 38.211532 148 0 0 32.442343 38.200622 149 0 0 32.386701 38.158449 150 0 0 32.354946 38.129865 151 0 0 32.333115 38.122791 152 0 0 32.322269 38.113463 153 0 0 32.298244 38.094669 154 0 0 32.308551 38.108583 155 0 0 32.302416 38.098731 156 0 0 32.362213 38.143613 157 0 0 32.402951 38.171377 158 0 0 32.418917 38.186351 159 0 0 32.481678 38.237022 160 0 0 32.507318 38.2575 161 0 0 32.532395 38.278253 162 0 0 32.594004 38.328289 163 0 0 32.594031 38.330892 164 0 0 32.594623 38.329236 165 0 0 32.648548 38.3694 166 0 0 32.629108 38.355365 167 0 0 32.624955 38.339236 168 0 0 32.583893 38.303291 169 0 0 32.543079 38.268722 170 0 0 32.523313 38.253184 171 0 0 32.502224 38.235069 172 0 0 32.517503 38.2547 173 0 0 32.519177 38.257535 174 0 0 32.542082 38.273832 175 0 0 32.537533 38.287345 176 0 0 32.573177 38.307541 177 0 0 32.649005 38.370677 178 0 0 32.676565 38.390824 179 0 0 32.712424 38.425794 180 0 0 32.792227 38.48462 181 0 0 32.813039 38.510533 182 0 0 32.840633 38.531876 183 0 0 32.907861 38.593753 184 0 0 32.959037 38.628447 185 0 0 32.945125 38.618984 186 0 0 32.989251 38.650918 187 0 0 32.984824 38.657726 188 0 0 33.035996 38.697468 189 0 0 33.050109 38.701764 190 0 0 33.089526 38.742936 191 0 0 33.038961 38.702794 192 0 0 33.008642 38.679608 193 0 0 32.990348 38.680616 194 0 0 32.937498 38.636531 195 0 0 32.898317 38.616472 196 0 0 32.926532 38.647297 197 0 0 32.939274 38.662574 198 0 0 32.922979 38.656353 199 0 0 32.899113 38.648789 200 0 0 32.882087 38.638056 201 0 0 32.863302 38.638414 202 0 0 32.864398 38.647903 203 0 0 32.861944 38.637238 204 0 0 32.843576 38.642525 205 0 0 32.845072 38.651952 206 0 0 32.839364 38.648135 207 0 0 32.787315 38.608266 208 0 0 32.777318 38.616491 209 0 0 32.834659 38.660807 210 0 0 32.741992 38.593175 211 0 0 32.712798 38.572637 212 0 0 32.765296 38.624648 213 0 0 32.67086 38.547986 214 0 0 32.653989 38.532644 215 0 0 32.665019 38.549991 216 0 0 32.626884 38.512178 217 0 0 32.547302 38.47174 218 0 0 32.660592 38.540332 219 0 0 32.535131 38.458917 220 0 0 32.559289 38.467396 221 0 0 32.53008 38.468126 222 0 0 32.524683 38.452602 223 0 0 32.464823 38.415295 224 0 0 32.493459 38.449826 225 0 0 32.533385 38.486754 226 0 0 32.375664 38.369597 227 0 0 32.534201 38.466416 228 0 0 32.397113 38.377429 229 0 0 32.359649 38.377581 230 0 0 32.330639 38.324057 231 0 0 32.332321 38.354558 232 0 0 32.344759 38.343578 233 0 0 32.391443 38.405564 234 0 0 32.305239 38.352624 235 0 0 32.271413 38.29353 236 0 0 32.222675 38.298639 237 0 0 32.218854 38.289936 238 0 0 32.235176 38.301433 239 0 0 32.170838 38.248825 240 0 0 32.08134 38.2115 241 0 0 32.033352 38.172107 242 0 0 32.019157 38.149336 243 0 0 32.008805 38.163634 244 0 0 32.023 38.156968 245 0 0 32.04432 38.171512 246 0 0 31.939558 38.128918 247 0 0 31.949744 38.09615 248 0 0 31.946348 38.097122 249 0 0 31.966869 38.127374 250 0 0 31.823284 38.010066 251 0 0 31.686773 37.943134 252 0 0 31.735982 37.97136 253 0 0 31.623829 37.925157 254 0 0 31.684541 37.946958 255 0 0 31.560392 37.866021 256 0 0 31.416585 37.75392 257 0 0 31.544815 37.875676 258 0 0 31.519181 37.844791 259 0 0 31.569846 37.884316 260 0 0 31.394087 37.729636 261 0 0 31.382119 37.73532 262 0 0 31.421966 37.806468 263 0 0 31.271312 37.666133 264 0 0 31.166741 37.646763 265 0 0 31.167149 37.617147 266 0 0 31.200342 37.644717 267 0 0 30.997616 37.49139 268 0 0 31.038661 37.547542 269 0 0 30.96518 37.486708 270 0 0 30.803215 37.366103 271 0 0 30.88935 37.414419 272 0 0 30.634968 37.267055 273 0 0 30.676539 37.276551 274 0 0 30.601103 37.247304 275 0 0 30.635148 37.290073 276 0 0 30.422167 37.122635 277 0 0 30.379953 37.077154 278 0 0 30.314953 37.073724 279 0 0 30.109397 36.949551 280 0 0 29.994519 36.86432 281 0 0 30.070024 36.893812 282 0 0 30.012184 36.782824 283 0 0 30.049943 36.860159 284 0 0 30.088531 36.920969 285 0 0 29.916927 36.778231 286 0 0 29.827723 36.662129 287 0 0 29.705418 36.64038 288 0 0 29.748423 36.660796 289 0 0 29.625578 36.559728 290 0 0 29.646893 36.630603 291 0 0 29.520632 36.555751 292 0 0 29.459106 36.476538 293 0 0 29.506153 36.497844 294 0 0 29.353076 36.363656 295 0 0 29.187564 36.262657 296 0 0 29.071504 36.213221 297 0 0 29.32219 36.348886 298 0 0 29.273323 36.317399 299 0 0 29.15493 36.243997 300 0 0 29.236059 36.267226 301 0 0 29.319224 36.358466 302 0 0 29.174815 36.266451 303 0 0 28.931641 36.218424 304 0 0 28.761589 35.992698 305 0 0 28.934232 36.142857 306 0 0 28.665718 35.861617 307 0 0 28.589976 35.865942 308 0 0 28.425806 35.646882 309 0 0 28.240602 35.510595 310 0 0 28.286439 35.647812 311 0 0 28.566067 35.895752 312 0 0 28.09916 35.531373 313 0 0 28.918822 36.078204 314 0 0 28.727713 35.845284 315 0 0 28.526151 35.704324 316 0 0 28.324324 35.561937 317 0 0 28.128362 35.447025 318 0 0 27.997326 35.409537 319 0 0 27.910819 35.30653 320 0 0 28.185484 35.647849 321 0 0 28.05151 35.447602 322 0 0 28.841487 36.001305 323 0 0 28.696703 35.874725 324 0 0 27.514354 35.209729 325 0 0 27.183463 34.945736 326 0 0 27.39255 35.008596 327 0 0 28.003226 35.356989 328 0 0 26.913669 34.365707 329 0 0 27.645418 34.796813 330 0 0 28.293578 35.747706 331 0 0 27.111111 34.878307 332 0 0 27.050314 35.050314 333 0 0 27.916667 35.148148 334 0 0 28.81203 35.977444 335 0 0 28.866071 35.735119 336 0 0 27.175258 34.742268 337 0 0 26.813187 34.930403 338 0 0 28.101266 35.594937 339 0 0 28.346667 35.6 340 0 0 29.641791 36.492537 341 0 0 24.964912 32.982456 342 0 0 29.392157 36.163399 343 0 0 29.227273 36.621212 344 0 0 27.74359 34.923077 345 0 0 29.933333 36.933333 346 0 0 27.423077 35.25641 347 0 0 28.714286 35.587302 348 0 0 26.833333 34.37037 349 0 0 29.642857 36.095238 350 0 0 22.461538 31.641026 351 0 0 30.166667 36.916667 352 0 0 24.833333 32.472222 353 0 0 27 33.555556 354 0 0 27.285714 34.333333 355 0 0 27.714286 36.190476 356 0 0 21 31.133333 357 0 0 22.25 31.75 358 0 0 27 36.5 359 0 0 19.75 31.25 360 0 0 19 31.333333 361 0 0 12 28.333333 362 0 0 18 33.333333 363 0 0 29 37