## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5384-Z0068-CGTCATTGCACAGAT/441525-L5384-Z0068-CGTCATTGCACAGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5384-Z0068-CGTCATTGCACAGAT/441525-L5384-Z0068-CGTCATTGCACAGAT_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 02:54:32 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 999348 999348 137 137683478 137683478 132772716 132772716 123490194 123490194 0 0 0.964333 0.896914 0 0.964333 0.896914 0 413050434 413050434 406549810 406549810 391708452 391708452 366480317 366480317 0.984262 0.948331 0.887253 0.984262 0.948331 0.887253 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 862 0 35.991458 40.993353 1 11716 0 35.982268 40.987706 2 14154 4800 35.993968 40.994993 3 35462 1323 35.983718 40.986656 4 57964 49796 35.992275 40.993698 5 115687 18016 35.995955 40.996632 6 112712 130009 35.97765 40.982023 7 203048 165085 35.983552 40.988899 8 195934 152490 35.990846 40.992463 9 247167 113774 35.964895 40.970847 10 254455 520683 35.885373 40.931037 11 300809 64164 35.923386 40.943192 12 350898 722292 35.317326 40.422442 13 351450 207447 33.931489 39.718499 14 456232 997112 35.887105 40.931656 15 375296 376183 35.802924 40.861069 16 379900 439080 35.779038 40.803909 17 520070 1102768 35.887488 40.906256 18 549257 734014 35.6974 40.749922 19 377689 701588 35.681602 40.762746 20 520120 999130 35.877515 40.918997 21 667512 1394764 35.805958 40.856876 22 328064 550685 35.558038 40.69541 23 1056770 1246074 35.225929 40.449539 24 584219 1212893 35.249841 40.483208 25 544323 481567 35.274794 40.505661 26 1768075 2537507 35.201503 40.442813 27 368840 898525 35.224519 40.471742 28 965707 405154 35.224986 40.47535 29 2478892 5115059 35.222289 40.469776 30 801477 41848 35.249934 40.489074 31 2409936 851470 35.240803 40.479696 32 1670833 5487089 35.226897 40.464196 33 879152 130207 35.241743 40.480418 34 2531053 2799276 35.246249 40.486333 35 2278868 3883239 35.267966 40.501615 36 112918875 2188963 35.283338 40.510762 37 0 4316295 35.28886 40.515278 38 0 405885 35.27488 40.507515 39 0 5123863 35.270556 40.504137 40 0 0 35.26436 40.496833 41 0 366480317 35.256749 40.492129 42 0 0 35.240251 40.479939 43 0 0 35.251736 40.488005 44 0 0 35.260759 40.494109 45 0 0 35.260902 40.494901 46 0 0 35.251516 40.487464 47 0 0 35.240673 40.479563 48 0 0 35.224808 40.467229 49 0 0 35.215331 40.461766 50 0 0 35.2235 40.467919 51 0 0 35.213687 40.461842 52 0 0 35.178707 40.438185 53 0 0 35.151727 40.426707 54 0 0 35.160255 40.431486 55 0 0 35.15708 40.427582 56 0 0 35.116696 40.407256 57 0 0 35.14624 40.417229 58 0 0 35.135667 40.406554 59 0 0 35.110096 40.386823 60 0 0 35.078754 40.364677 61 0 0 35.043196 40.336275 62 0 0 35.0019 40.306474 63 0 0 34.954461 40.271289 64 0 0 34.91515 40.23809 65 0 0 34.860462 40.20106 66 0 0 34.808469 40.162913 67 0 0 34.74375 40.113147 68 0 0 34.67566 40.06333 69 0 0 34.597942 40.003591 70 0 0 34.518959 39.940772 71 0 0 34.430303 39.873957 72 0 0 34.341926 39.801205 73 0 0 34.236106 39.716649 74 0 0 34.152106 39.650425 75 0 0 34.053272 39.570538 76 0 0 33.957094 39.495327 77 0 0 33.864403 39.425902 78 0 0 33.770697 39.352658 79 0 0 33.691652 39.291488 80 0 0 33.611786 39.225099 81 0 0 33.526528 39.156308 82 0 0 33.445983 39.093562 83 0 0 33.392825 39.048125 84 0 0 33.345349 39.007874 85 0 0 33.301422 38.973892 86 0 0 33.260565 38.938154 87 0 0 33.217651 38.904965 88 0 0 33.179388 38.871425 89 0 0 33.134941 38.83293 90 0 0 33.09355 38.795764 91 0 0 33.053071 38.760829 92 0 0 33.020442 38.731869 93 0 0 32.99223 38.703678 94 0 0 32.960173 38.676448 95 0 0 32.933263 38.653082 96 0 0 32.914383 38.637112 97 0 0 32.882904 38.609738 98 0 0 32.876108 38.605772 99 0 0 32.886046 38.612933 100 0 0 32.899742 38.621754 101 0 0 32.93151 38.645369 102 0 0 32.966953 38.673102 103 0 0 32.996797 38.693718 104 0 0 33.015147 38.708221 105 0 0 33.050169 38.731702 106 0 0 33.063954 38.741061 107 0 0 33.080897 38.755128 108 0 0 33.086351 38.757958 109 0 0 33.08623 38.759283 110 0 0 33.076935 38.75044 111 0 0 33.053824 38.733956 112 0 0 33.019381 38.701811 113 0 0 32.980505 38.666515 114 0 0 32.928132 38.623391 115 0 0 32.876138 38.583635 116 0 0 32.851967 38.56514 117 0 0 32.825319 38.547013 118 0 0 32.805847 38.533825 119 0 0 32.811779 38.543833 120 0 0 32.802925 38.536942 121 0 0 32.825447 38.555564 122 0 0 32.833905 38.557833 123 0 0 32.830048 38.551234 124 0 0 32.861749 38.577168 125 0 0 32.874651 38.581538 126 0 0 32.887503 38.589353 127 0 0 32.907407 38.604401 128 0 0 32.909739 38.602732 129 0 0 32.913797 38.606229 130 0 0 32.912725 38.602448 131 0 0 32.895185 38.588017 132 0 0 32.897649 38.592163 133 0 0 32.886425 38.57779 134 0 0 32.888566 38.576725 135 0 0 32.878158 38.566819 136 0 0 32.870406 38.560741 137 0 0 32.868661 38.557796 138 0 0 32.865374 38.561447 139 0 0 32.860784 38.558393 140 0 0 32.889728 38.579419 141 0 0 32.911949 38.598631 142 0 0 32.938543 38.619285 143 0 0 32.942944 38.62573 144 0 0 32.961858 38.637572 145 0 0 32.937334 38.614861 146 0 0 32.917374 38.590047 147 0 0 32.910426 38.587898 148 0 0 32.873548 38.555213 149 0 0 32.854194 38.539589 150 0 0 32.843087 38.533553 151 0 0 32.810903 38.503953 152 0 0 32.799806 38.49655 153 0 0 32.790804 38.489353 154 0 0 32.774299 38.475477 155 0 0 32.796919 38.492835 156 0 0 32.796732 38.494592 157 0 0 32.803306 38.492147 158 0 0 32.821863 38.513412 159 0 0 32.841369 38.522907 160 0 0 32.852686 38.530514 161 0 0 32.871785 38.550502 162 0 0 32.901683 38.571193 163 0 0 32.893441 38.564123 164 0 0 32.934822 38.600969 165 0 0 32.926702 38.59017 166 0 0 32.902823 38.572262 167 0 0 32.888498 38.555715 168 0 0 32.834044 38.502482 169 0 0 32.791126 38.468782 170 0 0 32.721338 38.412221 171 0 0 32.667949 38.36979 172 0 0 32.657344 38.358866 173 0 0 32.636031 38.339883 174 0 0 32.606401 38.315235 175 0 0 32.61041 38.321215 176 0 0 32.614073 38.325061 177 0 0 32.647301 38.3573 178 0 0 32.693544 38.388713 179 0 0 32.713594 38.412879 180 0 0 32.770496 38.453977 181 0 0 32.792698 38.475764 182 0 0 32.819383 38.49354 183 0 0 32.873509 38.534773 184 0 0 32.895325 38.55623 185 0 0 32.944945 38.599549 186 0 0 32.949578 38.604567 187 0 0 33.013022 38.656434 188 0 0 33.043907 38.678949 189 0 0 33.045079 38.679515 190 0 0 33.059017 38.69079 191 0 0 33.04991 38.686129 192 0 0 33.030848 38.680902 193 0 0 32.994798 38.655588 194 0 0 32.997762 38.658585 195 0 0 32.985398 38.655292 196 0 0 32.967521 38.647151 197 0 0 32.990365 38.662854 198 0 0 32.952832 38.647828 199 0 0 32.93053 38.643675 200 0 0 32.891946 38.619077 201 0 0 32.875083 38.615793 202 0 0 32.871204 38.618941 203 0 0 32.844479 38.600343 204 0 0 32.827851 38.60152 205 0 0 32.78313 38.572034 206 0 0 32.7386 38.548748 207 0 0 32.73276 38.551054 208 0 0 32.717743 38.539816 209 0 0 32.679992 38.520341 210 0 0 32.611945 38.47629 211 0 0 32.564333 38.444001 212 0 0 32.57332 38.458697 213 0 0 32.554701 38.449691 214 0 0 32.555041 38.451471 215 0 0 32.514543 38.423208 216 0 0 32.468014 38.40735 217 0 0 32.420715 38.362428 218 0 0 32.408234 38.362839 219 0 0 32.40261 38.36604 220 0 0 32.39668 38.356605 221 0 0 32.388198 38.352092 222 0 0 32.382413 38.343015 223 0 0 32.29236 38.285227 224 0 0 32.275267 38.268533 225 0 0 32.284137 38.283775 226 0 0 32.240951 38.259581 227 0 0 32.17977 38.20381 228 0 0 32.217846 38.235483 229 0 0 32.129726 38.181073 230 0 0 32.131154 38.174736 231 0 0 32.131109 38.190146 232 0 0 32.082483 38.1632 233 0 0 32.029125 38.119578 234 0 0 32.085697 38.164241 235 0 0 32.044365 38.122217 236 0 0 32.042493 38.136794 237 0 0 31.988979 38.101038 238 0 0 31.955573 38.076563 239 0 0 32.015608 38.119881 240 0 0 31.908889 38.043864 241 0 0 31.868688 38.024529 242 0 0 31.997516 38.112958 243 0 0 31.904572 38.049907 244 0 0 31.800443 37.986041 245 0 0 31.818602 37.978054 246 0 0 31.782258 37.977439 247 0 0 31.600252 37.846755 248 0 0 31.571757 37.835247 249 0 0 31.54906 37.832108 250 0 0 31.577327 37.838346 251 0 0 31.660993 37.916813 252 0 0 31.708844 37.951715 253 0 0 31.567478 37.869586 254 0 0 31.464612 37.79926 255 0 0 31.502802 37.824066 256 0 0 31.297732 37.694224 257 0 0 31.283496 37.669062 258 0 0 31.392192 37.753994 259 0 0 31.327021 37.707653 260 0 0 31.198967 37.626297 261 0 0 31.174903 37.583099 262 0 0 31.168306 37.600314 263 0 0 31.124285 37.565551 264 0 0 30.899186 37.41135 265 0 0 30.816486 37.353469 266 0 0 30.878922 37.392191 267 0 0 30.707785 37.280784 268 0 0 30.637934 37.267762 269 0 0 30.583881 37.251931 270 0 0 30.566222 37.240711 271 0 0 30.581084 37.257851 272 0 0 30.528052 37.239891 273 0 0 30.249317 36.997074 274 0 0 30.19426 36.973978 275 0 0 30.033587 36.844907 276 0 0 30.178488 36.984168 277 0 0 29.971961 36.828039 278 0 0 29.882897 36.79287 279 0 0 29.863901 36.801056 280 0 0 29.551799 36.52446 281 0 0 29.67443 36.634044 282 0 0 29.659717 36.576577 283 0 0 29.247998 36.3433 284 0 0 29.648122 36.588781 285 0 0 29.559155 36.518465 286 0 0 29.128584 36.246101 287 0 0 29.146096 36.259656 288 0 0 29.248355 36.325548 289 0 0 29.335859 36.451946 290 0 0 29.429295 36.404581 291 0 0 29.159108 36.233182 292 0 0 29.076312 36.139375 293 0 0 28.8597 36.074799 294 0 0 28.688073 35.881316 295 0 0 28.549886 35.831891 296 0 0 28.72549 36.025825 297 0 0 29.044066 36.112502 298 0 0 28.688064 35.999116 299 0 0 28.687674 36.014873 300 0 0 28.832646 36.112748 301 0 0 28.347015 35.612355 302 0 0 28.098806 35.597701 303 0 0 28.09737 35.565743 304 0 0 28.138113 35.545912 305 0 0 28.665587 35.958704 306 0 0 29.010372 36.180928 307 0 0 28.685424 35.915437 308 0 0 28.207473 35.623074 309 0 0 28.813094 36.091869 310 0 0 28.005814 35.375969 311 0 0 28.26518 35.553077 312 0 0 28.426649 35.764917 313 0 0 27.982759 35.5 314 0 0 27.707504 35.305768 315 0 0 27.814145 35.305921 316 0 0 27.205986 34.993545 317 0 0 27.552182 35.103099 318 0 0 27.928425 35.484663 319 0 0 27.909292 35.279499 320 0 0 28.242206 35.589928 321 0 0 27.307292 35.124132 322 0 0 26.95389 34.635927 323 0 0 27.981073 35.351209 324 0 0 27.660839 35.071096 325 0 0 27.711027 35.029151 326 0 0 27.034632 34.877345 327 0 0 27.369159 34.788162 328 0 0 26.803109 34.442142 329 0 0 27.479042 35.117764 330 0 0 27.748299 35.365079 331 0 0 26.530303 34.560606 332 0 0 28.170732 35.617886 333 0 0 27.08 34.59 334 0 0 27.967391 35.09058 335 0 0 27.691358 35.057613 336 0 0 26.890411 34.958904 337 0 0 27.621212 35.242424 338 0 0 27.387097 34.935484 339 0 0 28.056604 35.496855 340 0 0 28.155556 35.214815 341 0 0 28.333333 35.416667 342 0 0 28.69697 35.363636 343 0 0 27.48 35.68 344 0 0 27.75 34.597222 345 0 0 28.055556 35.592593 346 0 0 25.153846 34.051282 347 0 0 27.916667 35.472222 348 0 0 27.2 34.466667 349 0 0 26.111111 34.185185 350 0 0 31.125 38.25 351 0 0 27.166667 35.777778 352 0 0 21.5 30.25 353 0 0 35.25 40.25 354 0 0 35 40.166667 355 0 0 31 38.25 356 0 0 25.333333 36.333333 357 0 0 34 39.333333 358 0 0 36 41 359 0 0 28 37.5 360 0 0 20.5 32.666667 361 0 0 19.5 30.5 362 0 0 26 34.833333 363 0 0 16 28 364 0 0 9 21.666667 365 0 0 7 20.333333