## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/data/Runs/415630/output/415630-20250125_0254/415630-L3449-Z0007-CGATTCATGCTCGAT/415630-L3449-Z0007-CGATTCATGCTCGAT_sample.recal.bam OUTPUT=/data/Runs/415630/output/415630-20250125_0254/415630-L3449-Z0007-CGATTCATGCTCGAT/415630-L3449-Z0007-CGATTCATGCTCGAT_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: Sun Jan 26 12:31:15 EST 2025 ## 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 811800 811800 228 185438608 185438608 179761697 179761697 167032065 167032065 0 0 0.969387 0.900741 0 0.969387 0.900741 0 556315824 556315824 549552045 549552045 530409739 530409739 500106772 500106772 0.987842 0.953433 0.898962 0.987842 0.953433 0.898962 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 1778 1 35.125133 40.321291 1 25291 4 32.283858 38.553187 2 32321 18733 33.338206 39.14849 3 65773 4527 33.588705 39.304966 4 86770 104706 33.639145 39.33745 5 215902 19509 33.648951 39.345674 6 77258 270931 33.681064 39.370803 7 310708 302057 33.684895 39.372965 8 132891 178664 33.707831 39.38729 9 261539 177167 33.731615 39.405897 10 301956 507546 33.742008 39.4134 11 339096 126184 33.746533 39.416888 12 388438 653282 33.764317 39.429985 13 270284 249106 33.801871 39.456508 14 621472 875300 33.852058 39.490983 15 487492 590482 33.856899 39.494616 16 332372 209780 33.859956 39.497238 17 642914 925100 33.87507 39.509332 18 676311 1117054 33.894566 39.521806 19 406345 433646 33.910463 39.530973 20 969373 921296 33.918875 39.538937 21 917145 1821210 33.954008 39.560218 22 542345 404567 33.96157 39.567738 23 2055631 2606380 33.987368 39.586069 24 850218 1436860 33.997292 39.591533 25 738297 627485 34.016966 39.607549 26 2352522 3860413 34.039551 39.622744 27 591975 1297839 34.050265 39.631059 28 951491 902789 34.060069 39.637967 29 2760635 5263467 34.070061 39.645889 30 953295 129576 34.073552 39.649312 31 2722575 1899628 34.08431 39.653953 32 3755744 4046721 34.089368 39.660698 33 967870 478024 34.107967 39.669424 34 3293283 6666745 34.115595 39.677522 35 2652623 2488500 34.13245 39.689907 36 152686675 5338155 34.149132 39.700191 37 0 2955734 34.154964 39.705691 38 0 919137 34.169678 39.716536 39 0 5380747 34.188291 39.727618 40 0 12 34.18841 39.729649 41 0 500106760 34.207151 39.741577 42 0 0 34.216403 39.748616 43 0 0 34.219628 39.752223 44 0 0 34.236761 39.761449 45 0 0 34.24862 39.773429 46 0 0 34.248829 39.772293 47 0 0 34.264076 39.781119 48 0 0 34.273706 39.78813 49 0 0 34.274917 39.788223 50 0 0 34.28394 39.795123 51 0 0 34.287986 39.798078 52 0 0 34.294734 39.804098 53 0 0 34.307404 39.811475 54 0 0 34.319078 39.823007 55 0 0 34.326442 39.825083 56 0 0 34.343359 39.838279 57 0 0 34.344516 39.839984 58 0 0 34.342251 39.839393 59 0 0 34.352066 39.845692 60 0 0 34.361629 39.850986 61 0 0 34.362815 39.85392 62 0 0 34.377612 39.860436 63 0 0 34.378044 39.862941 64 0 0 34.381988 39.865735 65 0 0 34.38839 39.870328 66 0 0 34.39373 39.872603 67 0 0 34.401091 39.878544 68 0 0 34.408053 39.882212 69 0 0 34.413578 39.886939 70 0 0 34.415097 39.88706 71 0 0 34.410087 39.884483 72 0 0 34.432013 39.898575 73 0 0 34.424035 39.893597 74 0 0 34.423253 39.893712 75 0 0 34.432046 39.897381 76 0 0 34.437554 39.902756 77 0 0 34.435708 39.90289 78 0 0 34.439496 39.902866 79 0 0 34.433464 39.898716 80 0 0 34.443259 39.907441 81 0 0 34.446016 39.909896 82 0 0 34.445384 39.908527 83 0 0 34.447188 39.908459 84 0 0 34.452872 39.913296 85 0 0 34.448921 39.911744 86 0 0 34.4554 39.916289 87 0 0 34.454007 39.91318 88 0 0 34.455323 39.914716 89 0 0 34.465693 39.92237 90 0 0 34.449685 39.911818 91 0 0 34.44955 39.912126 92 0 0 34.462361 39.921366 93 0 0 34.466178 39.921323 94 0 0 34.465389 39.922085 95 0 0 34.465895 39.921653 96 0 0 34.468226 39.923299 97 0 0 34.469208 39.924606 98 0 0 34.466037 39.921829 99 0 0 34.463321 39.921738 100 0 0 34.469612 39.925145 101 0 0 34.473495 39.92867 102 0 0 34.476749 39.93055 103 0 0 34.483292 39.933583 104 0 0 34.481944 39.935039 105 0 0 34.475107 39.928143 106 0 0 34.478929 39.9324 107 0 0 34.480602 39.934553 108 0 0 34.473042 39.928937 109 0 0 34.491134 39.941331 110 0 0 34.491953 39.940216 111 0 0 34.483555 39.93458 112 0 0 34.484021 39.935914 113 0 0 34.480262 39.932178 114 0 0 34.492916 39.941427 115 0 0 34.490968 39.940701 116 0 0 34.495723 39.945753 117 0 0 34.491441 39.941947 118 0 0 34.503608 39.9507 119 0 0 34.498409 39.945394 120 0 0 34.503692 39.94948 121 0 0 34.501919 39.947976 122 0 0 34.504495 39.951106 123 0 0 34.505283 39.951881 124 0 0 34.506534 39.95231 125 0 0 34.505077 39.949954 126 0 0 34.505149 39.952521 127 0 0 34.499741 39.950927 128 0 0 34.501553 39.950028 129 0 0 34.499439 39.94833 130 0 0 34.495741 39.945977 131 0 0 34.5037 39.951107 132 0 0 34.493646 39.94514 133 0 0 34.504929 39.950365 134 0 0 34.509204 39.956361 135 0 0 34.508504 39.9556 136 0 0 34.514196 39.959645 137 0 0 34.509571 39.955947 138 0 0 34.5167 39.961651 139 0 0 34.514149 39.960234 140 0 0 34.512999 39.959887 141 0 0 34.516231 39.960759 142 0 0 34.514617 39.961627 143 0 0 34.517095 39.963503 144 0 0 34.525558 39.970164 145 0 0 34.520227 39.967287 146 0 0 34.51715 39.964015 147 0 0 34.521673 39.967198 148 0 0 34.516724 39.964433 149 0 0 34.518561 39.965682 150 0 0 34.51301 39.96059 151 0 0 34.520052 39.966677 152 0 0 34.520108 39.96816 153 0 0 34.514926 39.965094 154 0 0 34.519052 39.969795 155 0 0 34.524482 39.972054 156 0 0 34.513897 39.966087 157 0 0 34.525416 39.974115 158 0 0 34.520013 39.967446 159 0 0 34.519257 39.968883 160 0 0 34.521956 39.970884 161 0 0 34.519354 39.969854 162 0 0 34.522236 39.972716 163 0 0 34.533477 39.978767 164 0 0 34.520704 39.970909 165 0 0 34.531628 39.978868 166 0 0 34.530708 39.978063 167 0 0 34.531593 39.980076 168 0 0 34.524843 39.975643 169 0 0 34.525655 39.976174 170 0 0 34.523337 39.97492 171 0 0 34.536962 39.983942 172 0 0 34.524421 39.975212 173 0 0 34.523408 39.977288 174 0 0 34.536431 39.985432 175 0 0 34.533889 39.985469 176 0 0 34.530026 39.982264 177 0 0 34.525218 39.981152 178 0 0 34.533469 39.987909 179 0 0 34.524467 39.982782 180 0 0 34.533434 39.987495 181 0 0 34.526315 39.983358 182 0 0 34.529685 39.987699 183 0 0 34.534217 39.991708 184 0 0 34.522946 39.984189 185 0 0 34.542899 39.999062 186 0 0 34.537686 39.995564 187 0 0 34.543286 40.001201 188 0 0 34.5268 39.989384 189 0 0 34.527808 39.990067 190 0 0 34.53401 39.997131 191 0 0 34.534635 39.99844 192 0 0 34.533926 39.996978 193 0 0 34.534198 39.998778 194 0 0 34.527281 39.994274 195 0 0 34.52788 40.000051 196 0 0 34.517392 39.99155 197 0 0 34.527926 39.999186 198 0 0 34.523969 39.996908 199 0 0 34.52571 39.996881 200 0 0 34.513274 39.9885 201 0 0 34.518481 39.992256 202 0 0 34.509077 39.992084 203 0 0 34.507148 39.988184 204 0 0 34.500626 39.98436 205 0 0 34.496503 39.981581 206 0 0 34.498771 39.984412 207 0 0 34.498035 39.987548 208 0 0 34.486961 39.978349 209 0 0 34.479712 39.972762 210 0 0 34.478618 39.973808 211 0 0 34.475856 39.968648 212 0 0 34.464112 39.962952 213 0 0 34.467355 39.964872 214 0 0 34.459396 39.961721 215 0 0 34.450545 39.956624 216 0 0 34.444969 39.949976 217 0 0 34.444099 39.951587 218 0 0 34.424803 39.93851 219 0 0 34.410039 39.927335 220 0 0 34.403692 39.922971 221 0 0 34.414351 39.931824 222 0 0 34.392697 39.914544 223 0 0 34.394732 39.91732 224 0 0 34.367601 39.901781 225 0 0 34.373267 39.904982 226 0 0 34.35528 39.890829 227 0 0 34.349735 39.887475 228 0 0 34.348245 39.888386 229 0 0 34.316666 39.865628 230 0 0 34.312717 39.862689 231 0 0 34.309462 39.861577 232 0 0 34.293024 39.848864 233 0 0 34.274098 39.836016 234 0 0 34.258207 39.824579 235 0 0 34.255466 39.824985 236 0 0 34.251048 39.819984 237 0 0 34.239966 39.814419 238 0 0 34.226617 39.807424 239 0 0 34.210653 39.789836 240 0 0 34.206423 39.790151 241 0 0 34.195177 39.780636 242 0 0 34.178216 39.770324 243 0 0 34.15408 39.753162 244 0 0 34.140444 39.744975 245 0 0 34.123851 39.733525 246 0 0 34.103469 39.716912 247 0 0 34.090171 39.713001 248 0 0 34.066194 39.692011 249 0 0 34.060906 39.689651 250 0 0 34.044738 39.682308 251 0 0 34.026676 39.664155 252 0 0 34.00217 39.647261 253 0 0 33.992586 39.640993 254 0 0 33.971923 39.626544 255 0 0 33.966448 39.622663 256 0 0 33.964801 39.623938 257 0 0 33.927002 39.60001 258 0 0 33.90876 39.586361 259 0 0 33.891813 39.571564 260 0 0 33.850951 39.54554 261 0 0 33.858103 39.548473 262 0 0 33.832894 39.534191 263 0 0 33.809117 39.519676 264 0 0 33.781137 39.498976 265 0 0 33.78364 39.49718 266 0 0 33.735422 39.464434 267 0 0 33.729608 39.460715 268 0 0 33.707795 39.445907 269 0 0 33.678701 39.428292 270 0 0 33.663194 39.415724 271 0 0 33.619463 39.385855 272 0 0 33.606247 39.381903 273 0 0 33.594154 39.371669 274 0 0 33.559424 39.343661 275 0 0 33.535366 39.332832 276 0 0 33.530235 39.33088 277 0 0 33.504623 39.304839 278 0 0 33.485122 39.298771 279 0 0 33.46125 39.283876 280 0 0 33.433224 39.263034 281 0 0 33.40278 39.237649 282 0 0 33.401103 39.242587 283 0 0 33.378427 39.222415 284 0 0 33.322543 39.18449 285 0 0 33.291076 39.168785 286 0 0 33.266234 39.141368 287 0 0 33.242299 39.134747 288 0 0 33.227553 39.1188 289 0 0 33.221532 39.119133 290 0 0 33.187716 39.103657 291 0 0 33.142788 39.067328 292 0 0 33.151954 39.069531 293 0 0 33.11535 39.046685 294 0 0 33.063853 39.007656 295 0 0 33.082727 39.024348 296 0 0 33.012092 38.986926 297 0 0 32.986618 38.966806 298 0 0 32.96352 38.952178 299 0 0 33.006095 38.976829 300 0 0 32.937922 38.936307 301 0 0 32.894075 38.91104 302 0 0 32.875145 38.902234 303 0 0 32.875119 38.897693 304 0 0 32.863367 38.890606 305 0 0 32.83444 38.876006 306 0 0 32.796469 38.868594 307 0 0 32.827692 38.866432 308 0 0 32.784746 38.836526 309 0 0 32.818112 38.876017 310 0 0 32.693163 38.77756 311 0 0 32.692466 38.784435 312 0 0 32.732001 38.813366 313 0 0 32.642996 38.742839 314 0 0 32.619835 38.726348 315 0 0 32.711736 38.794418 316 0 0 32.611211 38.727665 317 0 0 32.628306 38.751054 318 0 0 32.581142 38.724467 319 0 0 32.764304 38.835952 320 0 0 32.603098 38.715017 321 0 0 32.576348 38.755928 322 0 0 32.618483 38.739393 323 0 0 32.613912 38.731868 324 0 0 32.796546 38.855939 325 0 0 32.615312 38.74896 326 0 0 32.731766 38.782349 327 0 0 32.714072 38.778643 328 0 0 32.581185 38.709631 329 0 0 32.426022 38.633086 330 0 0 32.608622 38.741195 331 0 0 32.561116 38.736606 332 0 0 32.439762 38.605799 333 0 0 32.618413 38.734908 334 0 0 32.535368 38.714286 335 0 0 32.347484 38.558438 336 0 0 32.299824 38.544386 337 0 0 32.382828 38.664983 338 0 0 32.512387 38.664039 339 0 0 32.682519 38.79563 340 0 0 32.765896 38.881021 341 0 0 33.115132 39.144189 342 0 0 32.603383 38.876566 343 0 0 32.828694 38.915774 344 0 0 32.660422 38.80484 345 0 0 32.772487 38.93739 346 0 0 32.406061 38.707071 347 0 0 33.131673 39.098458 348 0 0 32.538462 38.738192 349 0 0 33.125 39.243827 350 0 0 32.054054 38.527928 351 0 0 32.424242 38.541414 352 0 0 32.2 38.675862 353 0 0 31.851562 38.005208 354 0 0 32.213675 38.905983 355 0 0 33.125 39.176282 356 0 0 31.736264 38.406593 357 0 0 32.662791 39.209302 358 0 0 31.96 38.413333 359 0 0 32.338235 38.730392 360 0 0 32.433333 38.772222 361 0 0 32.517857 38.958333 362 0 0 34.28 40.086667 363 0 0 32.782609 39.094203 364 0 0 33.658537 39.203252 365 0 0 31.447368 38.105263 366 0 0 33.638889 39.611111 367 0 0 32.411765 38.460784 368 0 0 34.357143 40.142857 369 0 0 33.259259 39.17284 370 0 0 31.521739 37.565217 371 0 0 33.052632 39 372 0 0 30.944444 38.222222 373 0 0 28.0625 35.395833 374 0 0 30.642857 37.619048 375 0 0 29.769231 36.564103 376 0 0 32.222222 38.666667 377 0 0 33.285714 38.809524 378 0 0 29 36.857143 379 0 0 31.166667 38.111111 380 0 0 29.6 37.6 381 0 0 33.5 39.75 382 0 0 29.333333 37.666667 383 0 0 24.666667 34.777778 384 0 0 32.666667 38.333333 385 0 0 26.666667 36.777778 386 0 0 36 41 387 0 0 31 38 388 0 0 36 41 389 0 0 31 38 390 0 0 36 41 391 0 0 23 32.666667 392 0 0 10 22