## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5413-Z0107-CATGCATGGTACGAT/441525-L5413-Z0107-CATGCATGGTACGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5413-Z0107-CATGCATGGTACGAT/441525-L5413-Z0107-CATGCATGGTACGAT_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 02:59:54 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 1000777 1000777 126 126427064 126427064 121591553 121591553 112525842 112525842 0 0 0.961753 0.890046 0 0.961753 0.890046 0 379281192 379281192 372869060 372869060 358352398 358352398 334160489 334160489 0.983094 0.94482 0.881036 0.983094 0.94482 0.881036 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 908 0 35.99481 40.996111 1 10900 0 35.988609 40.992185 2 13391 4190 35.993396 40.994325 3 33864 1122 35.972492 40.976934 4 55416 47034 35.990708 40.992449 5 108814 17298 35.995419 40.996197 6 112724 121825 35.978981 40.983107 7 193342 155457 35.981552 40.987597 8 193058 148062 35.988684 40.990742 9 235973 108778 35.96163 40.967412 10 247571 507327 35.803706 40.88931 11 290888 60431 35.865123 40.897363 12 346066 701007 35.099226 40.24664 13 351257 206179 33.428361 39.411533 14 449866 978714 35.829718 40.892761 15 367140 371699 35.854022 40.898497 16 381498 444778 35.832154 40.854488 17 519813 1111205 35.902039 40.918359 18 547685 723944 35.686197 40.738354 19 375337 703082 35.687617 40.763239 20 498946 1009796 35.880306 40.919677 21 658388 1354791 35.833795 40.880534 22 321024 558993 35.597397 40.726116 23 1013806 1195238 35.297665 40.520154 24 574668 1173118 35.285117 40.517478 25 533242 473901 35.294855 40.524164 26 1716539 2482974 35.220705 40.468375 27 357944 860322 35.239976 40.484866 28 942121 382457 35.26285 40.501715 29 2449033 5025072 35.259225 40.497169 30 748569 38577 35.256659 40.494118 31 2321235 786633 35.248797 40.488156 32 1577279 5394222 35.241015 40.481073 33 819525 120870 35.244853 40.484504 34 2419859 2581359 35.242247 40.481873 35 2144795 3796869 35.249319 40.487275 36 102494580 2052209 35.277072 40.506254 37 0 4186780 35.272509 40.50497 38 0 342615 35.265469 40.500039 39 0 4891775 35.263851 40.499094 40 0 0 35.262523 40.496004 41 0 334160489 35.251258 40.488812 42 0 0 35.240588 40.480849 43 0 0 35.241345 40.480925 44 0 0 35.254739 40.490121 45 0 0 35.252122 40.487889 46 0 0 35.243523 40.483246 47 0 0 35.234683 40.476977 48 0 0 35.227141 40.471785 49 0 0 35.214932 40.462596 50 0 0 35.21611 40.463294 51 0 0 35.204341 40.455871 52 0 0 35.191962 40.446185 53 0 0 35.174238 40.434962 54 0 0 35.158386 40.422855 55 0 0 35.141371 40.409546 56 0 0 35.112885 40.390773 57 0 0 35.107924 40.384829 58 0 0 35.068346 40.357137 59 0 0 35.034221 40.331725 60 0 0 34.988052 40.299127 61 0 0 34.936743 40.259086 62 0 0 34.882805 40.220894 63 0 0 34.817646 40.170568 64 0 0 34.748858 40.119602 65 0 0 34.67876 40.065803 66 0 0 34.592607 40.001178 67 0 0 34.500688 39.935088 68 0 0 34.40065 39.86002 69 0 0 34.278703 39.764751 70 0 0 34.160685 39.671564 71 0 0 34.036415 39.570505 72 0 0 33.898495 39.459158 73 0 0 33.756827 39.346447 74 0 0 33.623542 39.241977 75 0 0 33.497575 39.139528 76 0 0 33.376574 39.046422 77 0 0 33.260601 38.960281 78 0 0 33.160294 38.882273 79 0 0 33.056152 38.799519 80 0 0 32.970347 38.731554 81 0 0 32.904112 38.675932 82 0 0 32.849639 38.629595 83 0 0 32.796101 38.584134 84 0 0 32.770962 38.559529 85 0 0 32.735968 38.529769 86 0 0 32.704023 38.502267 87 0 0 32.671129 38.475026 88 0 0 32.630185 38.436475 89 0 0 32.59506 38.40637 90 0 0 32.565509 38.376185 91 0 0 32.512512 38.332358 92 0 0 32.493529 38.31009 93 0 0 32.456882 38.280251 94 0 0 32.430627 38.254013 95 0 0 32.411687 38.238288 96 0 0 32.390301 38.218762 97 0 0 32.369451 38.202433 98 0 0 32.384904 38.213441 99 0 0 32.401393 38.228457 100 0 0 32.442924 38.260441 101 0 0 32.497967 38.303867 102 0 0 32.549362 38.344968 103 0 0 32.587006 38.370155 104 0 0 32.622692 38.394985 105 0 0 32.638324 38.404858 106 0 0 32.642902 38.404105 107 0 0 32.657935 38.417003 108 0 0 32.651317 38.408442 109 0 0 32.631798 38.391889 110 0 0 32.606508 38.373093 111 0 0 32.576332 38.348182 112 0 0 32.518152 38.30258 113 0 0 32.468209 38.261354 114 0 0 32.401017 38.207382 115 0 0 32.363306 38.180878 116 0 0 32.334948 38.156113 117 0 0 32.317936 38.143318 118 0 0 32.310382 38.139068 119 0 0 32.316749 38.150813 120 0 0 32.331965 38.162331 121 0 0 32.366097 38.186162 122 0 0 32.388376 38.205725 123 0 0 32.402395 38.213601 124 0 0 32.424045 38.227059 125 0 0 32.448316 38.245426 126 0 0 32.43903 38.233621 127 0 0 32.444185 38.231191 128 0 0 32.429553 38.217274 129 0 0 32.384565 38.178061 130 0 0 32.366746 38.160602 131 0 0 32.350954 38.148596 132 0 0 32.33195 38.132269 133 0 0 32.332359 38.132781 134 0 0 32.316803 38.120677 135 0 0 32.328025 38.12699 136 0 0 32.31483 38.116209 137 0 0 32.326388 38.118545 138 0 0 32.324482 38.12291 139 0 0 32.335109 38.12874 140 0 0 32.366398 38.161635 141 0 0 32.403133 38.186615 142 0 0 32.435539 38.212984 143 0 0 32.430438 38.208665 144 0 0 32.4448 38.218341 145 0 0 32.418634 38.19234 146 0 0 32.388086 38.163311 147 0 0 32.377955 38.153003 148 0 0 32.341486 38.115567 149 0 0 32.289923 38.078084 150 0 0 32.266721 38.065593 151 0 0 32.234311 38.034134 152 0 0 32.213969 38.017225 153 0 0 32.205533 38.017765 154 0 0 32.19582 38.004382 155 0 0 32.202535 38.015176 156 0 0 32.233763 38.03401 157 0 0 32.240175 38.039867 158 0 0 32.283891 38.073478 159 0 0 32.323095 38.097472 160 0 0 32.384842 38.153786 161 0 0 32.406564 38.169499 162 0 0 32.44729 38.199888 163 0 0 32.475912 38.226187 164 0 0 32.50341 38.251524 165 0 0 32.525773 38.261751 166 0 0 32.543854 38.276182 167 0 0 32.522147 38.250235 168 0 0 32.477142 38.207583 169 0 0 32.452446 38.197973 170 0 0 32.4375 38.179197 171 0 0 32.422455 38.16303 172 0 0 32.396327 38.156391 173 0 0 32.382479 38.147733 174 0 0 32.455465 38.212249 175 0 0 32.466436 38.209615 176 0 0 32.501013 38.246228 177 0 0 32.52256 38.260541 178 0 0 32.571696 38.305921 179 0 0 32.668435 38.37969 180 0 0 32.680245 38.384613 181 0 0 32.720816 38.431885 182 0 0 32.787311 38.486166 183 0 0 32.794887 38.495613 184 0 0 32.854894 38.545873 185 0 0 32.903318 38.584425 186 0 0 32.967446 38.639416 187 0 0 32.955143 38.621525 188 0 0 32.950435 38.625528 189 0 0 32.960714 38.632725 190 0 0 32.988144 38.651142 191 0 0 32.94305 38.633978 192 0 0 32.90241 38.591902 193 0 0 32.904764 38.603902 194 0 0 32.87069 38.580495 195 0 0 32.842899 38.576695 196 0 0 32.862631 38.593445 197 0 0 32.894523 38.622587 198 0 0 32.893806 38.628815 199 0 0 32.862795 38.604471 200 0 0 32.861164 38.621463 201 0 0 32.863091 38.612445 202 0 0 32.77923 38.566523 203 0 0 32.809186 38.594105 204 0 0 32.835558 38.626314 205 0 0 32.744638 38.557771 206 0 0 32.795005 38.605204 207 0 0 32.740299 38.573951 208 0 0 32.730733 38.561082 209 0 0 32.722621 38.565065 210 0 0 32.661758 38.528812 211 0 0 32.688384 38.536385 212 0 0 32.649252 38.52018 213 0 0 32.546679 38.456012 214 0 0 32.56582 38.473963 215 0 0 32.552307 38.465874 216 0 0 32.49438 38.426802 217 0 0 32.418227 38.362079 218 0 0 32.48482 38.424782 219 0 0 32.426515 38.369138 220 0 0 32.412957 38.362434 221 0 0 32.399663 38.343966 222 0 0 32.502972 38.439808 223 0 0 32.379001 38.362141 224 0 0 32.376555 38.342302 225 0 0 32.350748 38.333526 226 0 0 32.254257 38.288667 227 0 0 32.318198 38.325556 228 0 0 32.282019 38.30988 229 0 0 32.150202 38.20355 230 0 0 32.153358 38.204504 231 0 0 32.239139 38.266412 232 0 0 32.186762 38.245715 233 0 0 32.159659 38.227377 234 0 0 32.217128 38.257579 235 0 0 32.203147 38.250115 236 0 0 32.070975 38.170661 237 0 0 32.078925 38.179003 238 0 0 32.182816 38.238285 239 0 0 31.905852 38.058948 240 0 0 31.954983 38.112101 241 0 0 31.95963 38.097363 242 0 0 32.015222 38.128415 243 0 0 31.98103 38.133333 244 0 0 31.821293 38.006149 245 0 0 31.749048 37.965886 246 0 0 31.967153 38.116535 247 0 0 31.78294 38.013583 248 0 0 31.805227 37.973099 249 0 0 31.625128 37.844399 250 0 0 31.779207 38.013686 251 0 0 31.652564 37.911233 252 0 0 31.533308 37.833018 253 0 0 31.397177 37.768411 254 0 0 31.545805 37.85806 255 0 0 31.549578 37.834669 256 0 0 31.542863 37.819988 257 0 0 31.393461 37.767982 258 0 0 31.430568 37.814539 259 0 0 31.342754 37.772136 260 0 0 31.226914 37.62823 261 0 0 31.148779 37.594184 262 0 0 31.260926 37.67225 263 0 0 31.229922 37.658519 264 0 0 31.115725 37.576412 265 0 0 31.084943 37.555114 266 0 0 31.06042 37.531718 267 0 0 30.954586 37.428271 268 0 0 31.084337 37.504685 269 0 0 30.788991 37.323737 270 0 0 30.761151 37.277419 271 0 0 30.863757 37.400904 272 0 0 30.481481 37.185978 273 0 0 30.712732 37.307261 274 0 0 30.700108 37.331416 275 0 0 30.845044 37.365878 276 0 0 30.451025 37.02164 277 0 0 30.429736 37.15515 278 0 0 30.181131 36.917994 279 0 0 30.20156 37.002326 280 0 0 30.246407 36.946886 281 0 0 29.789222 36.662321 282 0 0 30.053292 36.864159 283 0 0 30.038943 36.905424 284 0 0 29.695798 36.72461 285 0 0 29.743056 36.688657 286 0 0 29.580645 36.60111 287 0 0 29.566078 36.628857 288 0 0 29.523307 36.523307 289 0 0 29.437931 36.400575 290 0 0 28.98806 36.043582 291 0 0 29.582053 36.435566 292 0 0 29.350225 36.436818 293 0 0 29.205179 36.32448 294 0 0 29.224066 36.307515 295 0 0 29.258967 36.354376 296 0 0 29.765056 36.713259 297 0 0 29.167572 36.238945 298 0 0 28.656631 35.923515 299 0 0 29.023609 36.198145 300 0 0 29.090667 36.149926 301 0 0 28.562324 35.899406 302 0 0 29.006924 36.090999 303 0 0 28.402706 35.777662 304 0 0 28.566886 35.810307 305 0 0 28.308227 35.568946 306 0 0 28.504305 35.810168 307 0 0 27.923077 35.301061 308 0 0 27.943423 35.480434 309 0 0 27.825564 35.270677 310 0 0 27.789727 35.280364 311 0 0 28.125862 35.433333 312 0 0 27.571429 35.107143 313 0 0 28.418033 35.909153 314 0 0 27.910714 35.30878 315 0 0 27.182033 34.982664 316 0 0 27.474227 35.036082 317 0 0 28.266476 35.684814 318 0 0 28.648903 35.729363 319 0 0 28.527211 35.99093 320 0 0 27.650558 35.183395 321 0 0 28.411765 35.371242 322 0 0 28.194915 35.649718 323 0 0 27.911628 35.362791 324 0 0 27.814433 35.221649 325 0 0 27.794118 35.531373 326 0 0 27.764706 34.88671 327 0 0 28.764286 36.019048 328 0 0 27 34.727778 329 0 0 28.654545 35.984848 330 0 0 26.533333 34.228571 331 0 0 28.347368 35.852632 332 0 0 26.855422 34.586345 333 0 0 28.333333 35.595556 334 0 0 28.106061 35.464646 335 0 0 27.483871 35.370968 336 0 0 26.06 34.72 337 0 0 26.25 34.641667 338 0 0 24.75 32.842593 339 0 0 27.685714 35.685714 340 0 0 24.483871 33.333333 341 0 0 26.172414 34 342 0 0 26.583333 33.986111 343 0 0 25.705882 33.686275 344 0 0 27.066667 34.266667 345 0 0 29.714286 37.261905 346 0 0 26 33.212121 347 0 0 35 40.272727 348 0 0 28.75 35.416667 349 0 0 24.142857 32.095238 350 0 0 33.4 39 351 0 0 34.333333 40 352 0 0 29.333333 37.666667 353 0 0 34 39.333333 354 0 0 34 39.333333 355 0 0 22.5 28.5 356 0 0 10.5 24.666667 357 0 0 32.5 39 358 0 0 11.5 19.666667 359 0 0 20.5 30 360 0 0 3 17.666667 361 0 0 14 25 362 0 0 26 33