## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5412-Z0106-CTGAGAATGTGTGAT/441525-L5412-Z0106-CTGAGAATGTGTGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5412-Z0106-CTGAGAATGTGTGAT/441525-L5412-Z0106-CTGAGAATGTGTGAT_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 02:56:40 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 1000707 1000707 133 134016571 134016571 128994406 128994406 119835135 119835135 0 0 0.962526 0.894181 0 0.962526 0.894181 0 402049713 402049713 395403044 395403044 380647588 380647588 356290563 356290563 0.983468 0.946767 0.886185 0.983468 0.946767 0.886185 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 989 0 35.992353 40.994205 1 12362 0 35.984688 40.989281 2 14514 4861 35.993945 40.994959 3 37962 1404 35.982046 40.985462 4 59968 52970 35.990575 40.992271 5 119961 19530 35.995058 40.995867 6 113367 135606 35.97879 40.982536 7 208295 171435 35.980477 40.986612 8 194993 156905 35.987902 40.990147 9 250741 120936 35.960678 40.967027 10 261557 520315 35.905185 40.942715 11 308636 68058 35.93706 40.953321 12 364714 731559 35.250187 40.365474 13 354997 218484 33.703622 39.576571 14 476064 1018413 35.898017 40.938612 15 384097 395737 35.808479 40.863856 16 393064 441263 35.765167 40.789632 17 524327 1126063 35.894657 40.910253 18 568530 760708 35.747207 40.793144 19 373027 702422 35.754802 40.823767 20 525106 988822 35.907962 40.940648 21 681132 1413834 35.827329 40.874934 22 329225 554246 35.591005 40.71688 23 1063649 1242196 35.295706 40.514894 24 593487 1229449 35.288409 40.516225 25 531235 478638 35.283992 40.513903 26 1741437 2538347 35.211724 40.459086 27 369116 886809 35.22049 40.469447 28 928588 398172 35.240371 40.482589 29 2396296 5024943 35.22851 40.475228 30 752500 42467 35.221787 40.46967 31 2283568 841444 35.206972 40.458849 32 1646236 5303429 35.202127 40.453044 33 830388 130187 35.200123 40.453372 34 2422006 2735966 35.200136 40.45202 35 2167740 3703453 35.216486 40.463732 36 109732697 2214663 35.234871 40.477253 37 0 4108758 35.237114 40.479807 38 0 392220 35.227363 40.474435 39 0 4884438 35.226036 40.4721 40 0 0 35.220424 40.468621 41 0 356290563 35.203722 40.455293 42 0 0 35.191028 40.44514 43 0 0 35.20099 40.451589 44 0 0 35.208001 40.456972 45 0 0 35.20363 40.454376 46 0 0 35.204288 40.455582 47 0 0 35.191357 40.445786 48 0 0 35.182918 40.438545 49 0 0 35.171246 40.432 50 0 0 35.172022 40.431844 51 0 0 35.161811 40.424778 52 0 0 35.138528 40.408492 53 0 0 35.126599 40.399805 54 0 0 35.113272 40.390258 55 0 0 35.096436 40.377515 56 0 0 35.068885 40.358094 57 0 0 35.060918 40.35239 58 0 0 35.033024 40.329757 59 0 0 34.993051 40.302571 60 0 0 34.955065 40.276218 61 0 0 34.914791 40.244821 62 0 0 34.86928 40.209955 63 0 0 34.820749 40.172268 64 0 0 34.758543 40.126497 65 0 0 34.694102 40.077964 66 0 0 34.642475 40.043099 67 0 0 34.562928 39.983128 68 0 0 34.47362 39.917117 69 0 0 34.395749 39.855294 70 0 0 34.292165 39.777272 71 0 0 34.199569 39.701268 72 0 0 34.090305 39.615885 73 0 0 33.98299 39.527337 74 0 0 33.869132 39.437047 75 0 0 33.776015 39.362723 76 0 0 33.657723 39.270142 77 0 0 33.55625 39.194937 78 0 0 33.452183 39.114738 79 0 0 33.363857 39.047022 80 0 0 33.281425 38.980542 81 0 0 33.212317 38.924926 82 0 0 33.156004 38.879049 83 0 0 33.097713 38.830176 84 0 0 33.061248 38.799235 85 0 0 33.026598 38.771957 86 0 0 33.0153 38.75895 87 0 0 32.981989 38.72813 88 0 0 32.953262 38.706625 89 0 0 32.920138 38.676039 90 0 0 32.887322 38.644378 91 0 0 32.865252 38.624272 92 0 0 32.83211 38.592422 93 0 0 32.803462 38.566996 94 0 0 32.778863 38.542693 95 0 0 32.75007 38.523032 96 0 0 32.731845 38.50699 97 0 0 32.708843 38.487433 98 0 0 32.704633 38.485826 99 0 0 32.707775 38.486869 100 0 0 32.728341 38.501985 101 0 0 32.760786 38.526899 102 0 0 32.798541 38.557523 103 0 0 32.833829 38.581466 104 0 0 32.881959 38.618598 105 0 0 32.919199 38.644673 106 0 0 32.935649 38.653855 107 0 0 32.952166 38.664626 108 0 0 32.961561 38.672883 109 0 0 32.970151 38.680272 110 0 0 32.957716 38.669853 111 0 0 32.948982 38.665338 112 0 0 32.916572 38.634507 113 0 0 32.892197 38.610491 114 0 0 32.8323 38.562283 115 0 0 32.792044 38.530486 116 0 0 32.754413 38.504176 117 0 0 32.750639 38.505659 118 0 0 32.753003 38.507475 119 0 0 32.764306 38.517884 120 0 0 32.776232 38.526623 121 0 0 32.773702 38.526189 122 0 0 32.797459 38.541015 123 0 0 32.807834 38.54924 124 0 0 32.843724 38.573341 125 0 0 32.870484 38.594423 126 0 0 32.892082 38.604263 127 0 0 32.904677 38.609408 128 0 0 32.902885 38.607146 129 0 0 32.891404 38.59786 130 0 0 32.882851 38.586949 131 0 0 32.854141 38.560364 132 0 0 32.85618 38.564604 133 0 0 32.855295 38.563062 134 0 0 32.845253 38.55394 135 0 0 32.85643 38.55466 136 0 0 32.853238 38.55026 137 0 0 32.825522 38.534005 138 0 0 32.83319 38.540618 139 0 0 32.847012 38.554606 140 0 0 32.875722 38.571832 141 0 0 32.921408 38.609194 142 0 0 32.931907 38.619226 143 0 0 32.930885 38.616759 144 0 0 32.912785 38.604973 145 0 0 32.914095 38.600202 146 0 0 32.873937 38.562907 147 0 0 32.854455 38.547374 148 0 0 32.832949 38.525636 149 0 0 32.798147 38.497628 150 0 0 32.764481 38.472296 151 0 0 32.708722 38.42713 152 0 0 32.708569 38.428735 153 0 0 32.679905 38.410349 154 0 0 32.688632 38.407265 155 0 0 32.670315 38.397741 156 0 0 32.664474 38.389819 157 0 0 32.716294 38.429558 158 0 0 32.718652 38.429843 159 0 0 32.723468 38.430629 160 0 0 32.788736 38.484389 161 0 0 32.799018 38.491441 162 0 0 32.804259 38.498856 163 0 0 32.852857 38.536055 164 0 0 32.854543 38.538914 165 0 0 32.848369 38.527981 166 0 0 32.838505 38.51638 167 0 0 32.785032 38.471825 168 0 0 32.742765 38.432932 169 0 0 32.704224 38.395273 170 0 0 32.640255 38.33965 171 0 0 32.602539 38.309041 172 0 0 32.57779 38.286891 173 0 0 32.55601 38.27578 174 0 0 32.58154 38.295465 175 0 0 32.59386 38.311367 176 0 0 32.596597 38.309643 177 0 0 32.630013 38.339272 178 0 0 32.676016 38.380844 179 0 0 32.723118 38.411018 180 0 0 32.758064 38.444097 181 0 0 32.7628 38.445924 182 0 0 32.855731 38.531872 183 0 0 32.904444 38.566833 184 0 0 32.959265 38.609365 185 0 0 32.987874 38.63859 186 0 0 33.01594 38.661238 187 0 0 33.062618 38.685279 188 0 0 33.100843 38.724958 189 0 0 33.102131 38.729762 190 0 0 33.093859 38.721249 191 0 0 33.098779 38.731436 192 0 0 33.092992 38.730765 193 0 0 33.04005 38.694945 194 0 0 33.058601 38.718058 195 0 0 33.006287 38.683741 196 0 0 32.980648 38.667144 197 0 0 32.997536 38.685008 198 0 0 32.964844 38.669502 199 0 0 32.961171 38.674882 200 0 0 32.953582 38.676513 201 0 0 32.947904 38.679239 202 0 0 32.919941 38.66288 203 0 0 32.883494 38.648014 204 0 0 32.860387 38.630788 205 0 0 32.808251 38.602806 206 0 0 32.761145 38.582681 207 0 0 32.789617 38.605943 208 0 0 32.717445 38.565605 209 0 0 32.676534 38.540412 210 0 0 32.695369 38.545606 211 0 0 32.651628 38.526285 212 0 0 32.665031 38.534275 213 0 0 32.556724 38.464122 214 0 0 32.649386 38.519859 215 0 0 32.612106 38.5104 216 0 0 32.557361 38.474986 217 0 0 32.594465 38.494898 218 0 0 32.534294 38.464538 219 0 0 32.443684 38.389146 220 0 0 32.51552 38.455973 221 0 0 32.401063 38.363322 222 0 0 32.402814 38.365798 223 0 0 32.382863 38.360539 224 0 0 32.447047 38.401511 225 0 0 32.384976 38.365158 226 0 0 32.334679 38.332031 227 0 0 32.39131 38.356869 228 0 0 32.392275 38.362756 229 0 0 32.323773 38.327901 230 0 0 32.365547 38.371348 231 0 0 32.278556 38.329212 232 0 0 32.292428 38.310236 233 0 0 32.325249 38.353483 234 0 0 32.240314 38.272695 235 0 0 32.223396 38.271823 236 0 0 32.155141 38.220092 237 0 0 32.175828 38.232512 238 0 0 32.243397 38.287584 239 0 0 32.18435 38.252115 240 0 0 32.18911 38.282031 241 0 0 32.008857 38.141322 242 0 0 32.041931 38.164984 243 0 0 32.090474 38.183083 244 0 0 32.042068 38.156173 245 0 0 31.949711 38.110729 246 0 0 31.932548 38.1 247 0 0 31.997005 38.15592 248 0 0 31.950439 38.114083 249 0 0 31.910766 38.090371 250 0 0 31.92305 38.089303 251 0 0 31.841854 38.071411 252 0 0 31.82844 38.04552 253 0 0 31.668752 37.916526 254 0 0 31.6537 37.922816 255 0 0 31.610733 37.905558 256 0 0 31.697633 37.968703 257 0 0 31.460011 37.795741 258 0 0 31.566584 37.873764 259 0 0 31.605086 37.903167 260 0 0 31.434799 37.794717 261 0 0 31.499087 37.841206 262 0 0 31.52799 37.84687 263 0 0 31.362941 37.735752 264 0 0 31.350707 37.739255 265 0 0 31.372578 37.796144 266 0 0 31.154708 37.630588 267 0 0 31.11894 37.6 268 0 0 30.997916 37.57223 269 0 0 30.941457 37.482486 270 0 0 31.05737 37.555875 271 0 0 30.907259 37.463703 272 0 0 30.834133 37.409719 273 0 0 30.832633 37.384859 274 0 0 30.842529 37.425535 275 0 0 30.708413 37.339452 276 0 0 30.825142 37.433196 277 0 0 30.807214 37.408951 278 0 0 30.501951 37.162183 279 0 0 30.506212 37.147961 280 0 0 30.396031 37.150273 281 0 0 30.30964 37.063083 282 0 0 30.200865 37.024216 283 0 0 30.048297 36.894774 284 0 0 30.008148 36.866842 285 0 0 30.23806 37.053996 286 0 0 30.071609 36.932271 287 0 0 29.81138 36.703126 288 0 0 30.121358 36.964181 289 0 0 29.960552 36.810207 290 0 0 29.754765 36.702703 291 0 0 29.765708 36.702192 292 0 0 29.578177 36.593823 293 0 0 29.425815 36.438258 294 0 0 29.618099 36.571055 295 0 0 29.260339 36.397062 296 0 0 29.207938 36.310619 297 0 0 29.393106 36.413764 298 0 0 28.701997 35.897977 299 0 0 28.806295 35.966774 300 0 0 28.823926 36.079472 301 0 0 28.837312 36.086354 302 0 0 28.805388 36.019508 303 0 0 28.651575 35.93914 304 0 0 28.916277 36.038135 305 0 0 28.461242 35.731537 306 0 0 28.709275 36.015656 307 0 0 28.706549 35.959488 308 0 0 28.879276 36.100827 309 0 0 28.399566 35.733382 310 0 0 28.645991 36.023197 311 0 0 28.680099 35.895285 312 0 0 28.970745 36.030733 313 0 0 28.739172 36.018287 314 0 0 28.568789 35.784052 315 0 0 28.477778 35.772593 316 0 0 28.06317 35.450934 317 0 0 29.03876 36.098622 318 0 0 28.128312 35.427243 319 0 0 28.977204 36.064843 320 0 0 27.659468 35.101883 321 0 0 28.050633 35.49789 322 0 0 28.467054 35.839147 323 0 0 28.051282 35.615385 324 0 0 27.414918 35.084693 325 0 0 27.528796 35.027051 326 0 0 28.147826 35.661836 327 0 0 28.15016 35.582535 328 0 0 28.325175 35.329837 329 0 0 28.03937 35.505249 330 0 0 27.38565 35.393124 331 0 0 28.199005 35.565506 332 0 0 27.683616 35.112994 333 0 0 27.231788 35.183223 334 0 0 28.924242 36.44697 335 0 0 26.793388 34.424242 336 0 0 27.514019 35.246106 337 0 0 27.453608 34.810997 338 0 0 28.413793 36.068966 339 0 0 27.246914 35.057613 340 0 0 26.028986 34.169082 341 0 0 29.163934 36.393443 342 0 0 28.4 35.442424 343 0 0 28.085106 35.205674 344 0 0 27.512195 34.715447 345 0 0 28.972222 35.935185 346 0 0 29.233333 36.133333 347 0 0 25.24 33.24 348 0 0 25.761905 33.873016 349 0 0 31.764706 37.862745 350 0 0 27.133333 34.311111 351 0 0 29.642857 36.285714 352 0 0 26.636364 33.939394 353 0 0 24 31.833333 354 0 0 29.25 34.916667 355 0 0 21 29.761905 356 0 0 24.166667 31.833333 357 0 0 24.166667 30.777778 358 0 0 26.5 35.333333 359 0 0 24 32.333333 360 0 0 33.5 39.5 361 0 0 33.5 39.5 362 0 0 15.5 22.5 363 0 0 24.5 36.333333 364 0 0 29 35.833333 365 0 0 34 39 366 0 0 32 38.166667 367 0 0 30.5 36.666667 368 0 0 26 34.166667