## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5382-Z0066-CAATGCACTCGAGAT/441525-L5382-Z0066-CAATGCACTCGAGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5382-Z0066-CAATGCACTCGAGAT/441525-L5382-Z0066-CAATGCACTCGAGAT_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 02:54:33 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 1000781 1000781 143 143504318 143504318 138521251 138521251 129048920 129048920 0 0 0.965276 0.899269 0 0.965276 0.899269 0 430512954 430512954 423932716 423932716 408830654 408830654 383293858 383293858 0.984715 0.949636 0.890319 0.984715 0.949636 0.890319 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 965 0 35.996249 40.997203 1 13143 0 35.98865 40.992561 2 15598 5331 35.994921 40.995792 3 39644 1434 35.975427 40.97968 4 61700 55199 35.98897 40.991009 5 123257 18238 35.994094 40.995041 6 113677 144087 35.97557 40.979434 7 212691 175450 35.970866 40.98053 8 196184 159372 35.983186 40.98581 9 251167 121613 35.94659 40.954952 10 263350 530194 35.880244 40.926852 11 305128 70172 35.915359 40.937391 12 356329 735196 35.262788 40.386694 13 346734 209895 33.874463 39.687315 14 468632 1004280 35.871016 40.920884 15 383868 389550 35.82014 40.872327 16 378585 424079 35.776888 40.803612 17 518837 1087922 35.885429 40.907788 18 553434 754420 35.690474 40.746933 19 380144 693806 35.689367 40.777302 20 540098 980710 35.886818 40.927337 21 683989 1413928 35.815602 40.868059 22 342662 545833 35.572515 40.710298 23 1111262 1317010 35.307536 40.534103 24 603889 1235872 35.287816 40.520669 25 560822 491793 35.266716 40.504323 26 1798345 2615385 35.21396 40.465468 27 378884 920247 35.2272 40.477447 28 973745 424987 35.243004 40.489326 29 2478635 5156297 35.235192 40.483398 30 808215 45385 35.231254 40.480123 31 2401859 908165 35.223236 40.472928 32 1771533 5435050 35.22601 40.47289 33 887939 141861 35.219183 40.469599 34 2568673 2963096 35.208104 40.46078 35 2301475 3827199 35.228188 40.476217 36 118309226 2348841 35.252744 40.491819 37 0 4253703 35.250112 40.491893 38 0 441995 35.238943 40.483167 39 0 5171501 35.245295 40.48828 40 0 1 35.236442 40.480562 41 0 383293857 35.21992 40.468415 42 0 0 35.214061 40.464622 43 0 0 35.211605 40.463439 44 0 0 35.225138 40.472134 45 0 0 35.215842 40.465894 46 0 0 35.216066 40.464751 47 0 0 35.210544 40.461246 48 0 0 35.19761 40.453115 49 0 0 35.195559 40.450099 50 0 0 35.189676 40.447894 51 0 0 35.182166 40.441197 52 0 0 35.173194 40.435545 53 0 0 35.166433 40.431824 54 0 0 35.159241 40.426071 55 0 0 35.14623 40.416499 56 0 0 35.131256 40.407149 57 0 0 35.121951 40.398529 58 0 0 35.104656 40.384478 59 0 0 35.072073 40.362325 60 0 0 35.049452 40.345091 61 0 0 35.017564 40.321284 62 0 0 34.981138 40.293611 63 0 0 34.943805 40.264763 64 0 0 34.903352 40.234339 65 0 0 34.857471 40.200674 66 0 0 34.809021 40.164203 67 0 0 34.759612 40.127125 68 0 0 34.694837 40.080226 69 0 0 34.632656 40.032987 70 0 0 34.569369 39.981651 71 0 0 34.495279 39.923845 72 0 0 34.422833 39.866846 73 0 0 34.345454 39.803149 74 0 0 34.278926 39.750866 75 0 0 34.187849 39.679174 76 0 0 34.111082 39.621622 77 0 0 34.039446 39.564819 78 0 0 33.959051 39.50381 79 0 0 33.891764 39.447928 80 0 0 33.822961 39.391912 81 0 0 33.75977 39.342324 82 0 0 33.688062 39.281288 83 0 0 33.644892 39.248703 84 0 0 33.588694 39.204029 85 0 0 33.548114 39.169177 86 0 0 33.508241 39.137791 87 0 0 33.46222 39.099113 88 0 0 33.433281 39.073926 89 0 0 33.389962 39.038024 90 0 0 33.348183 39.000648 91 0 0 33.295225 38.955322 92 0 0 33.275014 38.93505 93 0 0 33.248876 38.914095 94 0 0 33.210289 38.881282 95 0 0 33.17877 38.854881 96 0 0 33.153321 38.833289 97 0 0 33.137444 38.820239 98 0 0 33.139066 38.82142 99 0 0 33.144606 38.826103 100 0 0 33.15542 38.832001 101 0 0 33.183331 38.85382 102 0 0 33.200503 38.864311 103 0 0 33.225149 38.881584 104 0 0 33.253575 38.900611 105 0 0 33.271216 38.916911 106 0 0 33.275672 38.91656 107 0 0 33.299563 38.934864 108 0 0 33.309269 38.942756 109 0 0 33.292542 38.929821 110 0 0 33.298843 38.931625 111 0 0 33.267012 38.908389 112 0 0 33.24116 38.88358 113 0 0 33.188831 38.841373 114 0 0 33.148808 38.806579 115 0 0 33.101249 38.768835 116 0 0 33.07946 38.752489 117 0 0 33.05388 38.733756 118 0 0 33.045242 38.731994 119 0 0 33.034566 38.726276 120 0 0 33.037887 38.733407 121 0 0 33.039018 38.73064 122 0 0 33.057299 38.742021 123 0 0 33.074026 38.757536 124 0 0 33.090995 38.764528 125 0 0 33.109431 38.774486 126 0 0 33.107294 38.771064 127 0 0 33.124743 38.78343 128 0 0 33.139214 38.792043 129 0 0 33.125374 38.783382 130 0 0 33.128062 38.781827 131 0 0 33.112316 38.768556 132 0 0 33.117418 38.772594 133 0 0 33.106296 38.760096 134 0 0 33.100714 38.75641 135 0 0 33.092544 38.744326 136 0 0 33.093414 38.746399 137 0 0 33.068637 38.728864 138 0 0 33.074916 38.736057 139 0 0 33.076847 38.737658 140 0 0 33.095826 38.754934 141 0 0 33.135183 38.78492 142 0 0 33.14442 38.788053 143 0 0 33.147489 38.793037 144 0 0 33.149823 38.791812 145 0 0 33.139291 38.783323 146 0 0 33.121001 38.767551 147 0 0 33.096902 38.741779 148 0 0 33.094388 38.739788 149 0 0 33.049717 38.703504 150 0 0 33.020786 38.680468 151 0 0 33.010361 38.677021 152 0 0 33.002648 38.668709 153 0 0 32.982851 38.651515 154 0 0 32.964009 38.636695 155 0 0 32.973295 38.643822 156 0 0 32.955571 38.62426 157 0 0 32.970189 38.639672 158 0 0 32.955639 38.622133 159 0 0 32.984665 38.642407 160 0 0 33.02489 38.678778 161 0 0 33.025584 38.678357 162 0 0 33.054785 38.701519 163 0 0 33.075559 38.720792 164 0 0 33.06219 38.710485 165 0 0 33.073363 38.715013 166 0 0 33.047247 38.689148 167 0 0 33.00847 38.658389 168 0 0 32.966914 38.621811 169 0 0 32.914849 38.578114 170 0 0 32.872104 38.537404 171 0 0 32.817778 38.492443 172 0 0 32.794739 38.473982 173 0 0 32.772749 38.45214 174 0 0 32.755676 38.443335 175 0 0 32.772529 38.455994 176 0 0 32.764133 38.449086 177 0 0 32.776749 38.464502 178 0 0 32.781163 38.463061 179 0 0 32.833296 38.503768 180 0 0 32.847985 38.515936 181 0 0 32.865933 38.530673 182 0 0 32.913756 38.575202 183 0 0 32.963936 38.611849 184 0 0 33.002519 38.648877 185 0 0 33.022969 38.663257 186 0 0 33.083689 38.707104 187 0 0 33.098882 38.719586 188 0 0 33.105431 38.724901 189 0 0 33.131687 38.74673 190 0 0 33.11492 38.735587 191 0 0 33.142385 38.762924 192 0 0 33.121961 38.746341 193 0 0 33.075573 38.722642 194 0 0 33.074409 38.718195 195 0 0 33.046127 38.706819 196 0 0 33.036838 38.705618 197 0 0 33.005518 38.682934 198 0 0 32.990637 38.679308 199 0 0 32.975407 38.670644 200 0 0 32.989264 38.68422 201 0 0 32.952519 38.668788 202 0 0 32.933305 38.659708 203 0 0 32.904918 38.642596 204 0 0 32.858314 38.618968 205 0 0 32.80802 38.58211 206 0 0 32.812212 38.597231 207 0 0 32.813323 38.59427 208 0 0 32.797298 38.585924 209 0 0 32.758226 38.571681 210 0 0 32.718224 38.544175 211 0 0 32.694916 38.529695 212 0 0 32.701525 38.53579 213 0 0 32.637092 38.502515 214 0 0 32.614526 38.487729 215 0 0 32.606685 38.482603 216 0 0 32.551144 38.453423 217 0 0 32.539311 38.437428 218 0 0 32.552378 38.453644 219 0 0 32.502111 38.416646 220 0 0 32.486247 38.408098 221 0 0 32.430502 38.369114 222 0 0 32.424432 38.370157 223 0 0 32.396728 38.358761 224 0 0 32.340836 38.312109 225 0 0 32.315943 38.294862 226 0 0 32.307611 38.293525 227 0 0 32.32189 38.303445 228 0 0 32.279889 38.279553 229 0 0 32.186671 38.204715 230 0 0 32.260014 38.265415 231 0 0 32.238328 38.249308 232 0 0 32.201887 38.229978 233 0 0 32.169301 38.225093 234 0 0 32.146905 38.206028 235 0 0 32.102483 38.173545 236 0 0 32.052842 38.136542 237 0 0 32.027331 38.135326 238 0 0 32.000856 38.096325 239 0 0 32.057886 38.155597 240 0 0 32.065335 38.159527 241 0 0 31.830508 38.002166 242 0 0 31.837573 38.006869 243 0 0 31.767662 37.967068 244 0 0 31.754213 37.942273 245 0 0 31.883166 38.062178 246 0 0 31.892535 38.057087 247 0 0 31.78295 37.98863 248 0 0 31.829793 38.012532 249 0 0 31.670653 37.915162 250 0 0 31.696953 37.923246 251 0 0 31.662165 37.916243 252 0 0 31.632706 37.887621 253 0 0 31.548537 37.832663 254 0 0 31.49362 37.792805 255 0 0 31.498875 37.816614 256 0 0 31.480009 37.789474 257 0 0 31.502547 37.815075 258 0 0 31.33297 37.696927 259 0 0 31.463794 37.766099 260 0 0 31.36744 37.716125 261 0 0 31.139752 37.578986 262 0 0 31.267483 37.665678 263 0 0 31.159933 37.615162 264 0 0 31.251906 37.650198 265 0 0 31.116123 37.553376 266 0 0 30.916225 37.415305 267 0 0 30.963855 37.483675 268 0 0 30.798345 37.385921 269 0 0 30.794923 37.358755 270 0 0 30.815424 37.369639 271 0 0 30.431881 37.108607 272 0 0 30.522683 37.189736 273 0 0 30.544493 37.197012 274 0 0 30.578733 37.197703 275 0 0 30.523419 37.162659 276 0 0 30.429873 37.13228 277 0 0 30.31655 37.023448 278 0 0 30.143652 36.944645 279 0 0 30.265976 37.021765 280 0 0 30.321451 37.056493 281 0 0 29.990177 36.795514 282 0 0 29.925038 36.732455 283 0 0 29.933889 36.835445 284 0 0 29.833633 36.756977 285 0 0 29.851962 36.716445 286 0 0 29.481808 36.512384 287 0 0 29.492095 36.533926 288 0 0 29.457856 36.463516 289 0 0 29.385805 36.387782 290 0 0 29.216228 36.29576 291 0 0 29.312699 36.402215 292 0 0 29.323146 36.397141 293 0 0 29.363276 36.40848 294 0 0 29.074122 36.291322 295 0 0 28.919159 36.129794 296 0 0 28.804513 36.053973 297 0 0 28.916765 36.19451 298 0 0 28.64726 35.9066 299 0 0 28.841678 36.026008 300 0 0 28.748037 36.034483 301 0 0 28.666307 35.95965 302 0 0 28.386702 35.639918 303 0 0 28.468687 35.726869 304 0 0 28.287307 35.636221 305 0 0 28.890752 36.029012 306 0 0 28.509489 35.798054 307 0 0 28.263131 35.561969 308 0 0 28.041459 35.51557 309 0 0 28.553381 35.937129 310 0 0 28.155084 35.408408 311 0 0 28 35.413785 312 0 0 28.034789 35.491241 313 0 0 27.987825 35.460768 314 0 0 28.319224 35.666373 315 0 0 27.982692 35.373397 316 0 0 28.740625 35.872222 317 0 0 28.22361 35.687476 318 0 0 28.040491 35.498978 319 0 0 27.962963 35.468254 320 0 0 27.908309 35.34575 321 0 0 28.420128 35.757721 322 0 0 27.569444 35.267361 323 0 0 28.176471 35.500316 324 0 0 27.656522 35.207971 325 0 0 28.183374 35.464548 326 0 0 27.820312 35.15625 327 0 0 27.336257 35.088694 328 0 0 28.311688 35.640693 329 0 0 28.172662 35.653477 330 0 0 27.624 34.993333 331 0 0 27.668161 35.42003 332 0 0 27.505102 35.154762 333 0 0 26.940476 34.369048 334 0 0 28.453947 35.708333 335 0 0 28 35.422222 336 0 0 28.415929 35.828909 337 0 0 27.970297 35.445545 338 0 0 26.73913 34.304348 339 0 0 29.444444 36.238683 340 0 0 28.768116 36.352657 341 0 0 29.112903 36.489247 342 0 0 25.685185 34.179012 343 0 0 27.808511 34.730496 344 0 0 27.634146 35.186992 345 0 0 29.941176 36.921569 346 0 0 29.833333 36.444444 347 0 0 29.68 37.08 348 0 0 27.619048 34.952381 349 0 0 24.6 33.433333 350 0 0 27.117647 33.803922 351 0 0 30.333333 37.533333 352 0 0 32.076923 37.615385 353 0 0 31 37.384615 354 0 0 29.833333 36.361111 355 0 0 28.666667 35.916667 356 0 0 26.916667 34.222222 357 0 0 26.545455 34.424242 358 0 0 28.272727 36.030303 359 0 0 23.2 30.5 360 0 0 29 36.333333 361 0 0 27.777778 36 362 0 0 23 32.375 363 0 0 29.875 37.208333 364 0 0 17 31.2 365 0 0 27.6 35.533333 366 0 0 22.25 30.833333 367 0 0 32.75 39.5 368 0 0 34.5 39.583333 369 0 0 26.5 35.75 370 0 0 28.5 36.5 371 0 0 31 38.5 372 0 0 22 31 373 0 0 5 21.666667 374 0 0 32.5 39 375 0 0 29 36 376 0 0 34 39 377 0 0 34 39 378 0 0 30.5 37.833333 379 0 0 35 39.666667 380 0 0 7 15.333333 381 0 0 36 41 382 0 0 36 41 383 0 0 36 40.333333 384 0 0 31 38 385 0 0 15 26.333333