## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/data/Runs/415630/output/415630-20250125_0254/415630-L3450-Z0010-CACTGCACGAATGAT/415630-L3450-Z0010-CACTGCACGAATGAT_sample.recal.bam OUTPUT=/data/Runs/415630/output/415630-20250125_0254/415630-L3450-Z0010-CACTGCACGAATGAT/415630-L3450-Z0010-CACTGCACGAATGAT_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 12:31:05 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 743686 743686 232 173236425 173236425 168349512 168349512 157158864 157158864 0 0 0.97179 0.907193 0 0.97179 0.907193 0 519709275 519709275 513877036 513877036 497137362 497137362 470672074 470672074 0.988778 0.956568 0.905645 0.988778 0.956568 0.905645 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 1562 2 35.135011 40.329714 1 21479 3 32.313827 38.574243 2 28108 16364 33.355233 39.160013 3 56995 3797 33.603928 39.320655 4 74581 89333 33.659301 39.354457 5 185243 16474 33.688765 39.373836 6 67202 232653 33.71599 39.393987 7 267488 260779 33.733038 39.404169 8 115113 155086 33.744987 39.412687 9 225078 152190 33.771522 39.434622 10 261403 437065 33.797031 39.451251 11 290627 107162 33.81662 39.466125 12 334306 566474 33.821255 39.472349 13 234379 217540 33.859721 39.498284 14 533464 754568 33.901079 39.525291 15 417048 505481 33.91086 39.529526 16 287114 181980 33.923477 39.541034 17 551119 796667 33.933977 39.549605 18 581304 959109 33.953697 39.561041 19 353300 379512 33.953206 39.563839 20 847581 804666 33.974678 39.576221 21 791044 1556377 33.998035 39.594008 22 472817 354909 34.031317 39.618204 23 1824329 2314904 34.041663 39.624701 24 730145 1222005 34.066003 39.640281 25 648345 545190 34.076975 39.649106 26 2090168 3407125 34.089473 39.659073 27 507747 1120750 34.096987 39.665816 28 822666 764741 34.116982 39.677747 29 2455806 4649007 34.125087 39.683546 30 818066 116419 34.139499 39.692751 31 2407393 1631627 34.153554 39.704437 32 3218223 3607423 34.167939 39.71678 33 865711 434857 34.171892 39.717328 34 2883060 5675770 34.183974 39.727141 35 2398504 2237336 34.199571 39.739058 36 144567907 4537798 34.221166 39.75273 37 0 2645315 34.229878 39.76069 38 0 825088 34.240308 39.765871 39 0 4753655 34.254036 39.774903 40 0 13 34.258053 39.778923 41 0 470672061 34.268932 39.785064 42 0 0 34.298007 39.805637 43 0 0 34.307345 39.811559 44 0 0 34.306456 39.812016 45 0 0 34.327354 39.826049 46 0 0 34.335587 39.831895 47 0 0 34.345288 39.839408 48 0 0 34.357885 39.849346 49 0 0 34.361932 39.850922 50 0 0 34.365942 39.854353 51 0 0 34.385957 39.867029 52 0 0 34.385559 39.86675 53 0 0 34.39462 39.876188 54 0 0 34.400446 39.875805 55 0 0 34.414058 39.887463 56 0 0 34.422385 39.893325 57 0 0 34.423218 39.893626 58 0 0 34.437558 39.90412 59 0 0 34.442088 39.906501 60 0 0 34.442971 39.908601 61 0 0 34.45644 39.916402 62 0 0 34.461218 39.92102 63 0 0 34.468183 39.925855 64 0 0 34.478209 39.932858 65 0 0 34.483886 39.937753 66 0 0 34.482511 39.936293 67 0 0 34.497355 39.945561 68 0 0 34.491569 39.94257 69 0 0 34.501966 39.951012 70 0 0 34.50859 39.952757 71 0 0 34.51318 39.955895 72 0 0 34.52062 39.961522 73 0 0 34.52166 39.960837 74 0 0 34.519834 39.959807 75 0 0 34.530071 39.966162 76 0 0 34.535098 39.969738 77 0 0 34.536308 39.972631 78 0 0 34.533838 39.971695 79 0 0 34.540561 39.973743 80 0 0 34.538966 39.973529 81 0 0 34.549617 39.981384 82 0 0 34.540459 39.975346 83 0 0 34.551682 39.981955 84 0 0 34.545443 39.97761 85 0 0 34.548365 39.979615 86 0 0 34.556049 39.985496 87 0 0 34.561671 39.988836 88 0 0 34.552609 39.983068 89 0 0 34.567182 39.990791 90 0 0 34.563411 39.988664 91 0 0 34.570671 39.993933 92 0 0 34.56832 39.995266 93 0 0 34.566736 39.992935 94 0 0 34.567156 39.993012 95 0 0 34.570911 39.995604 96 0 0 34.576374 39.99826 97 0 0 34.585524 40.007316 98 0 0 34.589254 40.007587 99 0 0 34.593285 40.013889 100 0 0 34.588876 40.00682 101 0 0 34.589959 40.007573 102 0 0 34.588231 40.008622 103 0 0 34.597372 40.012841 104 0 0 34.598278 40.01335 105 0 0 34.600245 40.014524 106 0 0 34.602426 40.017219 107 0 0 34.606367 40.019932 108 0 0 34.596086 40.013663 109 0 0 34.603951 40.019074 110 0 0 34.603885 40.017143 111 0 0 34.612309 40.023981 112 0 0 34.60265 40.01803 113 0 0 34.608778 40.023056 114 0 0 34.614285 40.025863 115 0 0 34.604713 40.020037 116 0 0 34.618051 40.028544 117 0 0 34.613634 40.02696 118 0 0 34.623722 40.033294 119 0 0 34.621723 40.030407 120 0 0 34.631948 40.038527 121 0 0 34.62098 40.031965 122 0 0 34.627156 40.035279 123 0 0 34.632917 40.039358 124 0 0 34.630492 40.037549 125 0 0 34.62768 40.036001 126 0 0 34.633809 40.039715 127 0 0 34.635039 40.042542 128 0 0 34.631079 40.038792 129 0 0 34.632875 40.042601 130 0 0 34.634877 40.041532 131 0 0 34.634401 40.041291 132 0 0 34.634672 40.043525 133 0 0 34.639175 40.045149 134 0 0 34.641277 40.047467 135 0 0 34.648871 40.053759 136 0 0 34.644353 40.049617 137 0 0 34.64968 40.053001 138 0 0 34.647532 40.051992 139 0 0 34.652188 40.054394 140 0 0 34.65137 40.055915 141 0 0 34.648104 40.053047 142 0 0 34.651187 40.05594 143 0 0 34.656871 40.060599 144 0 0 34.662599 40.063258 145 0 0 34.65918 40.062916 146 0 0 34.658653 40.063051 147 0 0 34.667269 40.066642 148 0 0 34.655606 40.062368 149 0 0 34.671012 40.070506 150 0 0 34.66067 40.065772 151 0 0 34.658333 40.061597 152 0 0 34.666099 40.068771 153 0 0 34.668451 40.070735 154 0 0 34.672055 40.073918 155 0 0 34.666166 40.069016 156 0 0 34.67873 40.077378 157 0 0 34.66558 40.070092 158 0 0 34.673203 40.075157 159 0 0 34.668167 40.072644 160 0 0 34.66603 40.071975 161 0 0 34.663711 40.06739 162 0 0 34.671136 40.075534 163 0 0 34.680232 40.081178 164 0 0 34.679474 40.081739 165 0 0 34.678326 40.080687 166 0 0 34.674822 40.08005 167 0 0 34.675866 40.080526 168 0 0 34.675608 40.079715 169 0 0 34.678478 40.083297 170 0 0 34.669965 40.077832 171 0 0 34.678945 40.083956 172 0 0 34.678653 40.085085 173 0 0 34.684566 40.088662 174 0 0 34.687841 40.09236 175 0 0 34.680632 40.087502 176 0 0 34.686404 40.091094 177 0 0 34.6849 40.090727 178 0 0 34.684656 40.091141 179 0 0 34.68143 40.089175 180 0 0 34.685332 40.095139 181 0 0 34.68655 40.09686 182 0 0 34.689426 40.096306 183 0 0 34.689194 40.09633 184 0 0 34.691881 40.101697 185 0 0 34.694082 40.104282 186 0 0 34.695029 40.102478 187 0 0 34.698745 40.106716 188 0 0 34.698091 40.107343 189 0 0 34.695737 40.106486 190 0 0 34.6967 40.10675 191 0 0 34.688685 40.105445 192 0 0 34.685257 40.103272 193 0 0 34.688338 40.106179 194 0 0 34.689614 40.10649 195 0 0 34.685876 40.107352 196 0 0 34.696643 40.113222 197 0 0 34.692111 40.111913 198 0 0 34.694984 40.112527 199 0 0 34.691798 40.111998 200 0 0 34.694698 40.113704 201 0 0 34.682746 40.107401 202 0 0 34.687812 40.109397 203 0 0 34.679002 40.106069 204 0 0 34.684112 40.107838 205 0 0 34.674204 40.102692 206 0 0 34.674211 40.103322 207 0 0 34.659868 40.095271 208 0 0 34.667562 40.099484 209 0 0 34.664932 40.099432 210 0 0 34.655122 40.093351 211 0 0 34.651528 40.092078 212 0 0 34.649272 40.089544 213 0 0 34.636438 40.081109 214 0 0 34.633998 40.078889 215 0 0 34.637429 40.081848 216 0 0 34.618456 40.06994 217 0 0 34.625269 40.073881 218 0 0 34.613734 40.065346 219 0 0 34.595941 40.054325 220 0 0 34.598275 40.054996 221 0 0 34.582316 40.045357 222 0 0 34.582278 40.044237 223 0 0 34.566952 40.03589 224 0 0 34.556547 40.027839 225 0 0 34.558951 40.028983 226 0 0 34.546639 40.021456 227 0 0 34.52269 40.006937 228 0 0 34.529209 40.009906 229 0 0 34.519946 40.003456 230 0 0 34.505855 39.992107 231 0 0 34.486402 39.98227 232 0 0 34.487365 39.981293 233 0 0 34.481247 39.977142 234 0 0 34.45886 39.961115 235 0 0 34.444466 39.950059 236 0 0 34.419796 39.935917 237 0 0 34.417136 39.933115 238 0 0 34.41944 39.93301 239 0 0 34.410745 39.928672 240 0 0 34.379642 39.907322 241 0 0 34.367047 39.897347 242 0 0 34.366297 39.899686 243 0 0 34.343361 39.884219 244 0 0 34.327997 39.87364 245 0 0 34.318429 39.866198 246 0 0 34.307187 39.85982 247 0 0 34.299855 39.854125 248 0 0 34.27751 39.834023 249 0 0 34.263814 39.823809 250 0 0 34.241518 39.811668 251 0 0 34.232984 39.806578 252 0 0 34.210792 39.791858 253 0 0 34.205911 39.78396 254 0 0 34.182916 39.771143 255 0 0 34.161473 39.758 256 0 0 34.152304 39.750599 257 0 0 34.120065 39.725938 258 0 0 34.108863 39.721224 259 0 0 34.094484 39.709936 260 0 0 34.072183 39.69553 261 0 0 34.074976 39.696459 262 0 0 34.026868 39.670335 263 0 0 34.027246 39.66507 264 0 0 34.000341 39.649084 265 0 0 33.976618 39.631414 266 0 0 33.947861 39.611277 267 0 0 33.934778 39.607131 268 0 0 33.903227 39.584419 269 0 0 33.895251 39.579607 270 0 0 33.857872 39.547658 271 0 0 33.857458 39.552423 272 0 0 33.826815 39.532239 273 0 0 33.79689 39.505702 274 0 0 33.776907 39.494311 275 0 0 33.743757 39.475177 276 0 0 33.738394 39.467564 277 0 0 33.716977 39.452743 278 0 0 33.683914 39.429851 279 0 0 33.662844 39.419438 280 0 0 33.643249 39.400796 281 0 0 33.606502 39.376736 282 0 0 33.579875 39.366033 283 0 0 33.563519 39.349526 284 0 0 33.507336 39.310371 285 0 0 33.51544 39.316794 286 0 0 33.490311 39.302295 287 0 0 33.495306 39.308654 288 0 0 33.416335 39.252762 289 0 0 33.381624 39.233134 290 0 0 33.375093 39.22117 291 0 0 33.32768 39.191727 292 0 0 33.30869 39.18787 293 0 0 33.287655 39.170134 294 0 0 33.3022 39.179966 295 0 0 33.231332 39.133314 296 0 0 33.220328 39.127676 297 0 0 33.199066 39.11872 298 0 0 33.162113 39.082534 299 0 0 33.189903 39.118031 300 0 0 33.145339 39.08067 301 0 0 33.126063 39.066952 302 0 0 33.064089 39.020007 303 0 0 33.039463 39.011066 304 0 0 33.063897 39.030926 305 0 0 32.956626 38.952665 306 0 0 32.977018 38.965116 307 0 0 32.979742 38.98815 308 0 0 32.940824 38.939033 309 0 0 32.933312 38.940324 310 0 0 32.917571 38.926293 311 0 0 32.905635 38.915383 312 0 0 32.871544 38.911457 313 0 0 32.846365 38.883491 314 0 0 32.864505 38.884676 315 0 0 32.790668 38.841247 316 0 0 32.828953 38.875709 317 0 0 32.895656 38.942837 318 0 0 32.718933 38.810994 319 0 0 32.869981 38.898863 320 0 0 32.864204 38.909759 321 0 0 32.801653 38.84253 322 0 0 32.754704 38.825865 323 0 0 32.711605 38.811066 324 0 0 32.779779 38.870462 325 0 0 32.77744 38.864308 326 0 0 32.742949 38.853561 327 0 0 32.706785 38.814912 328 0 0 32.608437 38.801514 329 0 0 32.56176 38.709762 330 0 0 32.653278 38.775375 331 0 0 32.771019 38.878729 332 0 0 32.730904 38.861282 333 0 0 32.899753 38.922963 334 0 0 32.658605 38.865767 335 0 0 32.485732 38.72733 336 0 0 32.516618 38.756503 337 0 0 32.694513 38.814087 338 0 0 32.184586 38.49223 339 0 0 32.843284 38.927861 340 0 0 32.583535 38.769572 341 0 0 32.719512 38.884824 342 0 0 32.847222 38.951646 343 0 0 32.262522 38.53483 344 0 0 32.357834 38.614442 345 0 0 32.634146 38.800443 346 0 0 32.722084 38.746898 347 0 0 32.936464 38.927256 348 0 0 31.909657 38.26999 349 0 0 32.868243 38.978604 350 0 0 32.05303 38.390152 351 0 0 32.612335 38.903084 352 0 0 31.971014 38.405797 353 0 0 32.289617 38.59745 354 0 0 32.195266 38.431953 355 0 0 32.720779 38.898268 356 0 0 32.425532 38.671395 357 0 0 32.852459 38.852459 358 0 0 32.108108 38.690691 359 0 0 32.807692 38.833333 360 0 0 32.340659 38.78022 361 0 0 33.012048 39.140562 362 0 0 32.589041 38.748858 363 0 0 31.6875 38.3125 364 0 0 32.566667 38.733333 365 0 0 33.473684 39.093567 366 0 0 32.48 38.68 367 0 0 30.888889 38 368 0 0 33.555556 39.527778 369 0 0 31.1 37.577778 370 0 0 32.172414 38.586207 371 0 0 34.36 39.586667 372 0 0 32.75 39.069444 373 0 0 31.652174 37.623188 374 0 0 33.619048 39.571429 375 0 0 32.882353 38.823529 376 0 0 34.75 40.083333 377 0 0 31.357143 37.357143 378 0 0 32.928571 38.904762 379 0 0 33.727273 39.606061 380 0 0 34.3 39.9 381 0 0 34.666667 40.148148 382 0 0 33.875 39.833333 383 0 0 29.375 35.708333 384 0 0 35 40.428571 385 0 0 31.857143 36.904762 386 0 0 34.666667 39.944444 387 0 0 36 41 388 0 0 34 40 389 0 0 36 41 390 0 0 27.5 37 391 0 0 36 41 392 0 0 36 41