## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5383-Z0067-CTTATGAGCGCTGAT/441525-L5383-Z0067-CTTATGAGCGCTGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5383-Z0067-CTTATGAGCGCTGAT/441525-L5383-Z0067-CTTATGAGCGCTGAT_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 02:59:58 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 1001900 1001900 137 137369599 137369599 132360754 132360754 123106201 123106201 0 0 0.963537 0.896168 0 0.963537 0.896168 0 412108797 412108797 405490498 405490498 390644011 390644011 365838088 365838088 0.98394 0.947915 0.887722 0.98394 0.947915 0.887722 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 1024 0 35.99192 40.993582 1 12582 0 35.983352 40.988264 2 15066 5091 35.994187 40.995095 3 38112 1391 35.98133 40.984557 4 61591 54046 35.990326 40.992092 5 121099 18984 35.995181 40.995998 6 113993 138571 35.978217 40.982487 7 208939 173517 35.982959 40.988249 8 197723 159103 35.989643 40.991526 9 248806 121236 35.962721 40.968691 10 262820 527990 35.888391 40.930547 11 305370 68966 35.935652 40.952848 12 361859 726632 35.197782 40.322501 13 351417 213368 33.656364 39.541854 14 474393 1010813 35.892643 40.935472 15 384870 390874 35.802431 40.85972 16 387217 438946 35.75749 40.783287 17 522885 1111361 35.885505 40.902398 18 563231 755327 35.701316 40.754354 19 375848 702083 35.705813 40.787073 20 528955 988995 35.895996 40.932992 21 679358 1414773 35.814305 40.866905 22 332060 548692 35.573144 40.707917 23 1079025 1263924 35.300958 40.525411 24 589850 1218403 35.284278 40.517 25 545337 477633 35.263315 40.500931 26 1756861 2560355 35.210774 40.461503 27 362527 882413 35.225949 40.474263 28 952699 403475 35.240821 40.485252 29 2427881 5087824 35.241263 40.484426 30 774836 44564 35.230969 40.478013 31 2311110 853071 35.224962 40.471385 32 1681805 5407799 35.217303 40.465625 33 863699 136638 35.216085 40.46482 34 2474263 2799189 35.205471 40.458316 35 2206371 3763746 35.220954 40.467921 36 112794117 2261198 35.242831 40.483415 37 0 4162878 35.249258 40.489522 38 0 406626 35.238525 40.48225 39 0 4970214 35.230252 40.475002 40 0 0 35.229298 40.473573 41 0 365838088 35.214988 40.462168 42 0 0 35.202522 40.45507 43 0 0 35.205762 40.45498 44 0 0 35.212139 40.460761 45 0 0 35.212318 40.460393 46 0 0 35.205336 40.455481 47 0 0 35.199041 40.451226 48 0 0 35.195155 40.447991 49 0 0 35.183256 40.44116 50 0 0 35.172036 40.432112 51 0 0 35.16865 40.429814 52 0 0 35.155479 40.421163 53 0 0 35.148323 40.416867 54 0 0 35.145521 40.413626 55 0 0 35.131407 40.40456 56 0 0 35.118912 40.394691 57 0 0 35.107937 40.385658 58 0 0 35.086065 40.371287 59 0 0 35.056866 40.348611 60 0 0 35.030306 40.330359 61 0 0 35.005506 40.310742 62 0 0 34.966076 40.281909 63 0 0 34.933332 40.256869 64 0 0 34.892157 40.227085 65 0 0 34.855025 40.200105 66 0 0 34.812513 40.170095 67 0 0 34.75964 40.12941 68 0 0 34.711537 40.096271 69 0 0 34.648078 40.04885 70 0 0 34.585806 39.999036 71 0 0 34.506442 39.938116 72 0 0 34.439613 39.883416 73 0 0 34.370648 39.82888 74 0 0 34.279517 39.756863 75 0 0 34.202167 39.696891 76 0 0 34.115876 39.629571 77 0 0 34.029834 39.565654 78 0 0 33.943264 39.497246 79 0 0 33.856632 39.43081 80 0 0 33.772395 39.362541 81 0 0 33.68317 39.290759 82 0 0 33.608481 39.227714 83 0 0 33.53149 39.167732 84 0 0 33.459319 39.110762 85 0 0 33.405436 39.069213 86 0 0 33.342841 39.017384 87 0 0 33.286933 38.971767 88 0 0 33.228421 38.924849 89 0 0 33.169758 38.874313 90 0 0 33.10918 38.824154 91 0 0 33.05955 38.77886 92 0 0 33.022762 38.748057 93 0 0 32.979065 38.710044 94 0 0 32.940658 38.676514 95 0 0 32.913764 38.651135 96 0 0 32.900552 38.641473 97 0 0 32.882746 38.623049 98 0 0 32.864035 38.608783 99 0 0 32.862947 38.609454 100 0 0 32.885344 38.623019 101 0 0 32.899198 38.634567 102 0 0 32.947636 38.669359 103 0 0 32.966345 38.682901 104 0 0 32.979866 38.688961 105 0 0 33.008876 38.708666 106 0 0 32.995039 38.696097 107 0 0 33.005561 38.704307 108 0 0 33.006691 38.702974 109 0 0 32.991255 38.69189 110 0 0 32.9741 38.677832 111 0 0 32.945539 38.655104 112 0 0 32.910077 38.626869 113 0 0 32.863366 38.585126 114 0 0 32.813445 38.543648 115 0 0 32.779149 38.514951 116 0 0 32.73957 38.487038 117 0 0 32.72 38.47457 118 0 0 32.708753 38.466226 119 0 0 32.727545 38.485234 120 0 0 32.712707 38.474065 121 0 0 32.73094 38.484326 122 0 0 32.729419 38.486633 123 0 0 32.753066 38.498551 124 0 0 32.760968 38.50367 125 0 0 32.765316 38.504672 126 0 0 32.780991 38.511842 127 0 0 32.794594 38.518684 128 0 0 32.798053 38.520532 129 0 0 32.767378 38.493424 130 0 0 32.747996 38.476892 131 0 0 32.722533 38.454164 132 0 0 32.723466 38.456051 133 0 0 32.713379 38.447119 134 0 0 32.71921 38.444171 135 0 0 32.712963 38.441129 136 0 0 32.70438 38.434618 137 0 0 32.678163 38.415463 138 0 0 32.699612 38.43268 139 0 0 32.713088 38.44273 140 0 0 32.732649 38.45933 141 0 0 32.763445 38.483965 142 0 0 32.778961 38.495042 143 0 0 32.787064 38.49943 144 0 0 32.776017 38.492016 145 0 0 32.773148 38.484533 146 0 0 32.738756 38.454106 147 0 0 32.712934 38.432816 148 0 0 32.67347 38.395662 149 0 0 32.64228 38.376794 150 0 0 32.606914 38.343576 151 0 0 32.588162 38.330542 152 0 0 32.565423 38.306349 153 0 0 32.553477 38.302154 154 0 0 32.549731 38.297682 155 0 0 32.540854 38.2885 156 0 0 32.547336 38.293673 157 0 0 32.552599 38.299852 158 0 0 32.595905 38.330373 159 0 0 32.635583 38.362318 160 0 0 32.664187 38.383993 161 0 0 32.688447 38.402724 162 0 0 32.725673 38.430985 163 0 0 32.71946 38.42826 164 0 0 32.752972 38.453863 165 0 0 32.754789 38.457284 166 0 0 32.744522 38.439985 167 0 0 32.74568 38.436107 168 0 0 32.674997 38.381897 169 0 0 32.630575 38.344107 170 0 0 32.612963 38.322509 171 0 0 32.569336 38.285565 172 0 0 32.531703 38.255509 173 0 0 32.55185 38.276357 174 0 0 32.540604 38.271288 175 0 0 32.553769 38.282452 176 0 0 32.597483 38.318241 177 0 0 32.621254 38.331654 178 0 0 32.661643 38.370218 179 0 0 32.696669 38.401573 180 0 0 32.745536 38.434612 181 0 0 32.77595 38.462604 182 0 0 32.831709 38.513506 183 0 0 32.869124 38.541899 184 0 0 32.920537 38.589241 185 0 0 32.93831 38.602216 186 0 0 32.977479 38.633049 187 0 0 33.021081 38.670944 188 0 0 33.032592 38.672392 189 0 0 33.038673 38.679948 190 0 0 33.045956 38.691257 191 0 0 33.045086 38.695339 192 0 0 33.019108 38.674535 193 0 0 32.989219 38.66413 194 0 0 32.971892 38.647468 195 0 0 32.929845 38.62555 196 0 0 32.933845 38.635273 197 0 0 32.914336 38.627881 198 0 0 32.918783 38.637989 199 0 0 32.935566 38.655458 200 0 0 32.916864 38.642869 201 0 0 32.891465 38.635931 202 0 0 32.87077 38.624429 203 0 0 32.841525 38.613481 204 0 0 32.845329 38.627107 205 0 0 32.77604 38.578235 206 0 0 32.741571 38.555142 207 0 0 32.736808 38.558978 208 0 0 32.70856 38.54455 209 0 0 32.722946 38.551285 210 0 0 32.702936 38.541426 211 0 0 32.68523 38.529992 212 0 0 32.67413 38.532307 213 0 0 32.657031 38.523069 214 0 0 32.62617 38.501626 215 0 0 32.591803 38.489919 216 0 0 32.576288 38.478602 217 0 0 32.554922 38.46953 218 0 0 32.467979 38.403413 219 0 0 32.49464 38.422041 220 0 0 32.404043 38.366032 221 0 0 32.477431 38.417963 222 0 0 32.408382 38.366843 223 0 0 32.420576 38.386437 224 0 0 32.410199 38.371384 225 0 0 32.375322 38.339372 226 0 0 32.389916 38.36899 227 0 0 32.241446 38.252577 228 0 0 32.22196 38.250572 229 0 0 32.273985 38.274246 230 0 0 32.249407 38.275551 231 0 0 32.136876 38.207965 232 0 0 32.178774 38.247761 233 0 0 32.129545 38.192227 234 0 0 32.107793 38.167019 235 0 0 32.111426 38.187501 236 0 0 32.081751 38.168128 237 0 0 32.113865 38.187966 238 0 0 32.0044 38.114431 239 0 0 32.119668 38.199977 240 0 0 31.945289 38.066856 241 0 0 32.030488 38.157223 242 0 0 32.002565 38.126208 243 0 0 31.941891 38.087931 244 0 0 31.846875 38.025046 245 0 0 31.862823 38.044162 246 0 0 31.855544 38.026192 247 0 0 31.724606 37.944661 248 0 0 31.694519 37.918717 249 0 0 31.657008 37.898585 250 0 0 31.687008 37.900449 251 0 0 31.700946 37.934747 252 0 0 31.682528 37.923533 253 0 0 31.694673 37.933999 254 0 0 31.625418 37.889857 255 0 0 31.492183 37.794145 256 0 0 31.442118 37.770605 257 0 0 31.387478 37.745241 258 0 0 31.329024 37.698074 259 0 0 31.457885 37.805076 260 0 0 31.306866 37.729588 261 0 0 31.172107 37.611319 262 0 0 31.1384 37.570978 263 0 0 31.111934 37.596251 264 0 0 31.131449 37.583793 265 0 0 30.920549 37.414878 266 0 0 30.967984 37.459893 267 0 0 31.030017 37.526433 268 0 0 30.963688 37.474067 269 0 0 30.757948 37.324538 270 0 0 30.881353 37.452541 271 0 0 30.753948 37.334143 272 0 0 30.683499 37.30115 273 0 0 30.550767 37.207938 274 0 0 30.562418 37.212264 275 0 0 30.40218 37.104341 276 0 0 30.330334 37.077451 277 0 0 30.280608 37.023487 278 0 0 30.245957 37.00175 279 0 0 30.063472 36.87903 280 0 0 30.072396 36.83189 281 0 0 30.001608 36.824219 282 0 0 29.986467 36.835154 283 0 0 29.906342 36.780564 284 0 0 29.75763 36.696168 285 0 0 29.623645 36.548356 286 0 0 29.519241 36.508613 287 0 0 29.328947 36.374428 288 0 0 29.253417 36.434343 289 0 0 29.232995 36.286652 290 0 0 29.610932 36.557663 291 0 0 29.414118 36.391485 292 0 0 29.089703 36.195812 293 0 0 29.147134 36.212121 294 0 0 29.08828 36.24239 295 0 0 28.791204 35.999868 296 0 0 29.043802 36.183333 297 0 0 28.876802 36.062618 298 0 0 28.826147 36.019113 299 0 0 29.125599 36.334612 300 0 0 28.553418 35.839494 301 0 0 28.630101 35.903904 302 0 0 28.773034 35.946629 303 0 0 28.672455 35.924152 304 0 0 28.882353 36.007379 305 0 0 28.620643 35.853664 306 0 0 28.57234 35.840662 307 0 0 28.547945 35.773212 308 0 0 28.145663 35.665848 309 0 0 28.32371 35.635171 310 0 0 29.024809 36.18416 311 0 0 27.986789 35.488482 312 0 0 28.326861 35.677095 313 0 0 27.91462 35.488889 314 0 0 28.25 35.641582 315 0 0 28.636238 35.926694 316 0 0 28.109445 35.398801 317 0 0 28.16 35.704533 318 0 0 27.448517 35.130308 319 0 0 28.370656 35.702703 320 0 0 27.35443 34.777778 321 0 0 28.278689 35.705699 322 0 0 27.797436 35.198291 323 0 0 27.677143 35.28381 324 0 0 28.246951 35.817073 325 0 0 27.756757 35.454955 326 0 0 28.460967 35.600991 327 0 0 27.263374 34.809328 328 0 0 29.378995 36.412481 329 0 0 27.494949 34.824916 330 0 0 27.215909 34.835227 331 0 0 29.354037 36.113872 332 0 0 27.544218 35.054422 333 0 0 28.226277 35.530414 334 0 0 27.285714 34.770308 335 0 0 28.554545 35.972727 336 0 0 28.087912 35.263736 337 0 0 27.329268 34.943089 338 0 0 28.642857 35.62381 339 0 0 27.285714 34.978836 340 0 0 28.035714 35.160714 341 0 0 27.87234 35.312057 342 0 0 26.102564 33.923077 343 0 0 27.451613 35.096774 344 0 0 25.413793 33.183908 345 0 0 25.115385 33.371795 346 0 0 27.16 34.52 347 0 0 28.73913 36.101449 348 0 0 26.043478 34.521739 349 0 0 26.65 34.583333 350 0 0 27.375 34 351 0 0 25.230769 34.179487 352 0 0 29.6 36.966667 353 0 0 24.4 33.833333 354 0 0 30.142857 38.047619 355 0 0 28.666667 35.833333 356 0 0 24.2 32.866667 357 0 0 27.4 34.8 358 0 0 21.333333 30.222222 359 0 0 21 32.444444 360 0 0 36 41 361 0 0 36 41 362 0 0 30.5 36.666667 363 0 0 35 40.166667 364 0 0 32 37.833333 365 0 0 26.5 36.333333 366 0 0 32 38 367 0 0 24 33.333333 368 0 0 18 28.333333