## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5277-Z0018-CATGCGTCCTGTGAT/441525-L5277-Z0018-CATGCGTCCTGTGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5277-Z0018-CATGCGTCCTGTGAT/441525-L5277-Z0018-CATGCGTCCTGTGAT_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 02:56:49 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 1001848 1001848 156 156615040 156615040 151979217 151979217 142580912 142580912 0 0 0.9704 0.910391 0 0.9704 0.910391 0 469845120 469845120 463797113 463797113 448956807 448956807 423041321 423041321 0.987128 0.955542 0.900385 0.987128 0.955542 0.900385 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 791 0 35.993811 40.99525 1 10874 0 35.985875 40.990346 2 13762 4773 35.993618 40.994486 3 33133 1282 35.977327 40.981335 4 52104 46148 35.989272 40.991353 5 105069 14896 35.994411 40.995439 6 99936 119432 35.977116 40.981515 7 185934 147688 35.98276 40.988104 8 175995 139624 35.988917 40.991218 9 227468 98595 35.945093 40.953913 10 232556 479227 35.907093 40.938705 11 275441 56710 35.940534 40.957 12 326036 671045 35.408059 40.509212 13 333131 182921 34.314574 39.954096 14 428623 926777 35.891108 40.933746 15 356380 351783 35.815502 40.869735 16 360385 389433 35.764111 40.792652 17 502979 1047603 35.901418 40.917466 18 532588 686964 35.703417 40.761884 19 382638 683106 35.778215 40.835712 20 523750 979641 35.922664 40.947078 21 654001 1344711 35.830406 40.875394 22 342906 555764 35.631626 40.749043 23 1075825 1287404 35.334482 40.528869 24 595920 1206933 35.420832 40.60182 25 547231 511995 35.423337 40.608571 26 1804473 2511487 35.355054 40.548826 27 377197 939808 35.395534 40.592448 28 969210 411966 35.398435 40.595899 29 2507792 5090597 35.385125 40.583392 30 830473 43901 35.416983 40.604751 31 2487908 934933 35.413165 40.601965 32 1743834 5404451 35.39419 40.582633 33 901241 131155 35.415659 40.60344 34 2619149 2909412 35.403804 40.597165 35 2450657 3917642 35.42363 40.610631 36 131547650 2267488 35.449212 40.627557 37 0 4442068 35.444357 40.626025 38 0 467466 35.440569 40.624425 39 0 5396970 35.438787 40.621392 40 0 6 35.424474 40.61088 41 0 423041315 35.422015 40.608518 42 0 0 35.410912 40.601742 43 0 0 35.422313 40.609796 44 0 0 35.428827 40.612762 45 0 0 35.43457 40.616715 46 0 0 35.42234 40.60692 47 0 0 35.415306 40.603145 48 0 0 35.395702 40.58883 49 0 0 35.398046 40.591136 50 0 0 35.407079 40.598316 51 0 0 35.40356 40.595628 52 0 0 35.372944 40.574428 53 0 0 35.350164 40.566946 54 0 0 35.363205 40.572766 55 0 0 35.365195 40.574749 56 0 0 35.32384 40.555662 57 0 0 35.365704 40.571791 58 0 0 35.36728 40.570252 59 0 0 35.355421 40.561679 60 0 0 35.338964 40.548442 61 0 0 35.325741 40.538899 62 0 0 35.300892 40.520845 63 0 0 35.279886 40.50451 64 0 0 35.260387 40.489711 65 0 0 35.233647 40.468957 66 0 0 35.204708 40.448889 67 0 0 35.166042 40.421454 68 0 0 35.129964 40.394907 69 0 0 35.088304 40.362609 70 0 0 35.04072 40.327268 71 0 0 34.993303 40.288582 72 0 0 34.930954 40.238378 73 0 0 34.878214 40.194594 74 0 0 34.821067 40.14996 75 0 0 34.755489 40.099433 76 0 0 34.695939 40.053673 77 0 0 34.632987 40.006982 78 0 0 34.566958 39.956707 79 0 0 34.499663 39.903251 80 0 0 34.442864 39.858499 81 0 0 34.38197 39.808596 82 0 0 34.32809 39.766454 83 0 0 34.275555 39.722694 84 0 0 34.219872 39.67788 85 0 0 34.173054 39.642312 86 0 0 34.130195 39.606946 87 0 0 34.08695 39.573731 88 0 0 34.045328 39.537484 89 0 0 33.988971 39.492822 90 0 0 33.955431 39.462405 91 0 0 33.91487 39.429982 92 0 0 33.875151 39.392745 93 0 0 33.851333 39.374313 94 0 0 33.827954 39.351704 95 0 0 33.797817 39.326899 96 0 0 33.787804 39.318214 97 0 0 33.772842 39.306894 98 0 0 33.767246 39.3001 99 0 0 33.784617 39.31361 100 0 0 33.799272 39.323799 101 0 0 33.808149 39.330345 102 0 0 33.835752 39.35255 103 0 0 33.854458 39.366059 104 0 0 33.866689 39.371671 105 0 0 33.865363 39.369064 106 0 0 33.867988 39.368576 107 0 0 33.849806 39.353235 108 0 0 33.84267 39.348391 109 0 0 33.822388 39.332809 110 0 0 33.798373 39.314195 111 0 0 33.766268 39.287736 112 0 0 33.724351 39.255242 113 0 0 33.665791 39.203951 114 0 0 33.613063 39.160156 115 0 0 33.565473 39.12505 116 0 0 33.524796 39.088984 117 0 0 33.505607 39.078167 118 0 0 33.492341 39.069166 119 0 0 33.484331 39.067017 120 0 0 33.48315 39.065771 121 0 0 33.478623 39.059777 122 0 0 33.47954 39.062306 123 0 0 33.459525 39.043049 124 0 0 33.465038 39.043362 125 0 0 33.483842 39.055182 126 0 0 33.475274 39.046505 127 0 0 33.471065 39.041849 128 0 0 33.480209 39.043963 129 0 0 33.442449 39.01384 130 0 0 33.42546 39.00081 131 0 0 33.405685 38.982878 132 0 0 33.398807 38.975771 133 0 0 33.393079 38.968904 134 0 0 33.383286 38.961063 135 0 0 33.371846 38.950533 136 0 0 33.373533 38.94892 137 0 0 33.352177 38.932993 138 0 0 33.344472 38.931058 139 0 0 33.34614 38.936094 140 0 0 33.362253 38.945515 141 0 0 33.384162 38.964593 142 0 0 33.390739 38.967689 143 0 0 33.381229 38.959275 144 0 0 33.380814 38.957533 145 0 0 33.357323 38.935637 146 0 0 33.326631 38.910617 147 0 0 33.297512 38.884393 148 0 0 33.269203 38.862374 149 0 0 33.244412 38.841924 150 0 0 33.1924 38.80081 151 0 0 33.163674 38.779559 152 0 0 33.148975 38.765663 153 0 0 33.13327 38.75155 154 0 0 33.131564 38.754195 155 0 0 33.133542 38.753824 156 0 0 33.132737 38.748415 157 0 0 33.166144 38.777252 158 0 0 33.175753 38.787147 159 0 0 33.198459 38.798868 160 0 0 33.231606 38.827525 161 0 0 33.270499 38.853406 162 0 0 33.277316 38.86512 163 0 0 33.290888 38.872818 164 0 0 33.297063 38.878852 165 0 0 33.280882 38.869614 166 0 0 33.267598 38.849757 167 0 0 33.25776 38.839255 168 0 0 33.20843 38.794914 169 0 0 33.161935 38.75661 170 0 0 33.109388 38.716047 171 0 0 33.095786 38.70024 172 0 0 33.094382 38.700416 173 0 0 33.097548 38.704279 174 0 0 33.099063 38.705636 175 0 0 33.102062 38.713538 176 0 0 33.127329 38.734378 177 0 0 33.15681 38.761848 178 0 0 33.192243 38.789745 179 0 0 33.231906 38.818813 180 0 0 33.278205 38.863366 181 0 0 33.303648 38.883474 182 0 0 33.351901 38.927022 183 0 0 33.391411 38.959919 184 0 0 33.40937 38.972156 185 0 0 33.433211 38.991005 186 0 0 33.462749 39.016785 187 0 0 33.485475 39.03456 188 0 0 33.469857 39.021338 189 0 0 33.49001 39.041888 190 0 0 33.46959 39.022806 191 0 0 33.468999 39.02781 192 0 0 33.4398 39.007705 193 0 0 33.433665 39.010626 194 0 0 33.383542 38.975124 195 0 0 33.377881 38.974842 196 0 0 33.378363 38.985366 197 0 0 33.369608 38.981743 198 0 0 33.352525 38.970232 199 0 0 33.370719 38.995065 200 0 0 33.356501 38.988786 201 0 0 33.35137 38.993189 202 0 0 33.333298 38.982638 203 0 0 33.300401 38.966222 204 0 0 33.28618 38.957949 205 0 0 33.281676 38.963596 206 0 0 33.25524 38.949541 207 0 0 33.232744 38.943544 208 0 0 33.235264 38.94383 209 0 0 33.211811 38.934205 210 0 0 33.188457 38.916088 211 0 0 33.171503 38.909102 212 0 0 33.133417 38.884562 213 0 0 33.124328 38.88084 214 0 0 33.07356 38.84565 215 0 0 33.065737 38.837346 216 0 0 33.045341 38.833577 217 0 0 33.056238 38.837975 218 0 0 33.02919 38.829225 219 0 0 33.012825 38.819809 220 0 0 33.007203 38.816158 221 0 0 32.944448 38.770355 222 0 0 32.914738 38.755531 223 0 0 32.911948 38.748717 224 0 0 32.899754 38.738063 225 0 0 32.860817 38.713774 226 0 0 32.874048 38.733394 227 0 0 32.800769 38.678323 228 0 0 32.851242 38.713394 229 0 0 32.779566 38.666001 230 0 0 32.79213 38.680186 231 0 0 32.735966 38.639502 232 0 0 32.717514 38.636678 233 0 0 32.707508 38.629623 234 0 0 32.720495 38.642748 235 0 0 32.700573 38.621027 236 0 0 32.615568 38.574571 237 0 0 32.616726 38.565008 238 0 0 32.591467 38.550136 239 0 0 32.583559 38.553842 240 0 0 32.521511 38.513023 241 0 0 32.496893 38.505565 242 0 0 32.476514 38.486771 243 0 0 32.406364 38.442098 244 0 0 32.410845 38.445781 245 0 0 32.422304 38.446229 246 0 0 32.365725 38.412681 247 0 0 32.344614 38.398504 248 0 0 32.287462 38.36184 249 0 0 32.309863 38.372557 250 0 0 32.187441 38.289772 251 0 0 32.16939 38.294653 252 0 0 32.151101 38.271139 253 0 0 32.172283 38.293546 254 0 0 32.141759 38.275735 255 0 0 32.082158 38.236066 256 0 0 31.995683 38.183144 257 0 0 31.987494 38.170137 258 0 0 31.922348 38.12948 259 0 0 31.90283 38.134474 260 0 0 31.969071 38.175806 261 0 0 31.895471 38.122867 262 0 0 31.828847 38.094209 263 0 0 31.73212 38.004336 264 0 0 31.703611 37.999415 265 0 0 31.620356 37.941307 266 0 0 31.625096 37.936617 267 0 0 31.583958 37.918434 268 0 0 31.608111 37.921179 269 0 0 31.462667 37.843457 270 0 0 31.46302 37.842929 271 0 0 31.33414 37.739447 272 0 0 31.267024 37.695992 273 0 0 31.276326 37.701768 274 0 0 31.230592 37.66865 275 0 0 31.117923 37.590647 276 0 0 31.061778 37.559418 277 0 0 31.038181 37.561824 278 0 0 30.912252 37.478182 279 0 0 30.889773 37.465843 280 0 0 30.811721 37.387436 281 0 0 30.606696 37.263931 282 0 0 30.635744 37.27674 283 0 0 30.624729 37.272982 284 0 0 30.520918 37.197784 285 0 0 30.335145 37.083129 286 0 0 30.361601 37.110123 287 0 0 30.292232 37.061481 288 0 0 30.221887 36.992083 289 0 0 30.113532 36.946315 290 0 0 30.146679 36.94268 291 0 0 30.0748 36.90535 292 0 0 29.855503 36.713723 293 0 0 29.78394 36.700907 294 0 0 29.846971 36.729614 295 0 0 29.728272 36.647048 296 0 0 29.601485 36.575589 297 0 0 29.568818 36.549235 298 0 0 29.498998 36.476105 299 0 0 29.460911 36.488855 300 0 0 29.295782 36.364464 301 0 0 29.323806 36.363003 302 0 0 29.382768 36.414463 303 0 0 29.272913 36.326028 304 0 0 29.227548 36.339261 305 0 0 29.033538 36.16322 306 0 0 29.08989 36.185222 307 0 0 28.962268 36.113092 308 0 0 28.917053 36.114167 309 0 0 28.913473 36.069167 310 0 0 28.873572 36.028416 311 0 0 29.025812 36.143373 312 0 0 28.794601 36.042232 313 0 0 28.793224 36.018007 314 0 0 28.787634 35.939489 315 0 0 28.699858 35.91995 316 0 0 28.552377 35.770841 317 0 0 28.785699 35.97337 318 0 0 28.5312 35.798833 319 0 0 28.471992 35.705937 320 0 0 28.516612 35.795842 321 0 0 28.45359 35.73866 322 0 0 28.34082 35.701172 323 0 0 28.346792 35.645398 324 0 0 28.423776 35.680226 325 0 0 27.994372 35.39798 326 0 0 28.411341 35.694538 327 0 0 28.413032 35.79842 328 0 0 28.104693 35.480746 329 0 0 28.347594 35.64639 330 0 0 27.973274 35.386785 331 0 0 28.472175 35.840079 332 0 0 28.483654 35.70609 333 0 0 27.912766 35.486879 334 0 0 28.577345 35.787657 335 0 0 27.447043 35.168271 336 0 0 27.496951 35.189024 337 0 0 27.509735 35.19705 338 0 0 28.015905 35.486415 339 0 0 28.176339 35.570685 340 0 0 28.307107 35.826565 341 0 0 27.982196 35.377844 342 0 0 27.905085 35.345763 343 0 0 27.695652 35.038208 344 0 0 28.008734 35.371179 345 0 0 27.169082 35.128824 346 0 0 27.111732 34.707635 347 0 0 29.125786 36.104822 348 0 0 27.419118 34.968137 349 0 0 27.533333 34.7 350 0 0 28.814815 35.996914 351 0 0 28.53125 35.711806 352 0 0 28.075 35.270833 353 0 0 29.642857 36.590476 354 0 0 28.2 35.872222 355 0 0 28.339286 35.505952 356 0 0 27.583333 35.513889 357 0 0 26.404762 34.349206 358 0 0 28.028571 36.028571 359 0 0 26.4 33.788889 360 0 0 21.88 31.64 361 0 0 29.875 36.875 362 0 0 28.565217 36.014493 363 0 0 29.3 37.166667 364 0 0 26.235294 34.705882 365 0 0 28.5625 35.645833 366 0 0 30 37.575758 367 0 0 28.666667 36.777778 368 0 0 35 40.277778 369 0 0 29.5 38.277778 370 0 0 26.75 34.083333 371 0 0 36 41 372 0 0 21 29.111111 373 0 0 32.666667 39.333333 374 0 0 36 41 375 0 0 21.666667 30.888889 376 0 0 25.666667 34 377 0 0 32 37 378 0 0 34.5 40 379 0 0 27 34.666667 380 0 0 36 41 381 0 0 36 41