## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5370-Z0038-CGCATCCTCACAGAT/441525-L5370-Z0038-CGCATCCTCACAGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5370-Z0038-CGCATCCTCACAGAT/441525-L5370-Z0038-CGCATCCTCACAGAT_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 03:02:05 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 999200 999200 130 130894181 130894181 125895943 125895943 116632229 116632229 0 0 0.961815 0.891042 0 0.961815 0.891042 0 392682543 392682543 386044967 386044967 371183342 371183342 346485444 346485444 0.983097 0.94525 0.882355 0.983097 0.94525 0.882355 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 929 0 35.990312 40.992684 1 11973 2 35.983805 40.988835 2 14578 4831 35.994182 40.995253 3 36993 1330 35.982795 40.986093 4 60024 50986 35.989321 40.991587 5 118289 18403 35.993879 40.994995 6 116567 134202 35.97515 40.979343 7 206320 168823 35.978767 40.985272 8 201557 157969 35.989369 40.991561 9 247615 117501 35.962464 40.968829 10 261276 531536 35.817501 40.896922 11 304552 66511 35.850983 40.887519 12 359777 733599 35.113597 40.281258 13 356155 216514 33.657089 39.558087 14 468547 1015192 35.823148 40.890641 15 381598 385295 35.821692 40.870942 16 386851 447979 35.762364 40.789329 17 529256 1127486 35.879731 40.898523 18 559145 751453 35.702552 40.751659 19 376236 707964 35.679865 40.757547 20 520957 1007717 35.878929 40.919322 21 682330 1406691 35.817339 40.867725 22 329842 554703 35.561223 40.701419 23 1056197 1243359 35.258355 40.496173 24 594141 1214260 35.24745 40.490621 25 551798 477308 35.245443 40.487111 26 1754732 2565372 35.176468 40.434056 27 371875 882121 35.198698 40.453484 28 961944 402211 35.214339 40.466454 29 2439898 5107883 35.210418 40.46185 30 772925 41935 35.21073 40.460939 31 2319014 827870 35.201207 40.452678 32 1661860 5431184 35.194406 40.446485 33 847313 133487 35.195966 40.448812 34 2452323 2747995 35.186861 40.441699 35 2184522 3791401 35.205242 40.455835 36 106394272 2170084 35.225323 40.469037 37 0 4180192 35.224697 40.469583 38 0 396903 35.217564 40.466804 39 0 4976847 35.216121 40.464458 40 0 0 35.210577 40.458274 41 0 346485444 35.19762 40.449033 42 0 0 35.187603 40.441665 43 0 0 35.186066 40.440969 44 0 0 35.195993 40.447844 45 0 0 35.194807 40.447403 46 0 0 35.194789 40.446911 47 0 0 35.186613 40.441078 48 0 0 35.172932 40.432062 49 0 0 35.167773 40.428525 50 0 0 35.160895 40.422851 51 0 0 35.152542 40.417513 52 0 0 35.132274 40.40357 53 0 0 35.127779 40.401853 54 0 0 35.114127 40.3916 55 0 0 35.092487 40.377719 56 0 0 35.067872 40.360148 57 0 0 35.05376 40.347215 58 0 0 35.021762 40.324933 59 0 0 34.97708 40.291671 60 0 0 34.928132 40.255159 61 0 0 34.878887 40.218102 62 0 0 34.802907 40.160043 63 0 0 34.739058 40.109076 64 0 0 34.671444 40.058696 65 0 0 34.583635 39.991129 66 0 0 34.498801 39.931378 67 0 0 34.39617 39.852132 68 0 0 34.301233 39.781968 69 0 0 34.194858 39.702724 70 0 0 34.086238 39.61486 71 0 0 33.976916 39.527566 72 0 0 33.874493 39.444188 73 0 0 33.776662 39.361946 74 0 0 33.66799 39.27833 75 0 0 33.571792 39.2018 76 0 0 33.481753 39.13126 77 0 0 33.407348 39.074645 78 0 0 33.341131 39.023083 79 0 0 33.261956 38.963945 80 0 0 33.210349 38.916187 81 0 0 33.167211 38.880275 82 0 0 33.114415 38.837406 83 0 0 33.082895 38.808654 84 0 0 33.051123 38.779347 85 0 0 33.024286 38.759386 86 0 0 32.992911 38.728783 87 0 0 32.958261 38.702365 88 0 0 32.915771 38.663043 89 0 0 32.877825 38.632469 90 0 0 32.834673 38.590993 91 0 0 32.783087 38.547583 92 0 0 32.757537 38.52481 93 0 0 32.717313 38.491394 94 0 0 32.684672 38.463772 95 0 0 32.67692 38.45473 96 0 0 32.659169 38.439803 97 0 0 32.634605 38.420506 98 0 0 32.638275 38.421524 99 0 0 32.660521 38.43863 100 0 0 32.694719 38.464056 101 0 0 32.738094 38.500237 102 0 0 32.777636 38.527884 103 0 0 32.816756 38.558751 104 0 0 32.842774 38.578498 105 0 0 32.876935 38.60196 106 0 0 32.873528 38.592404 107 0 0 32.882384 38.600905 108 0 0 32.883441 38.600406 109 0 0 32.861069 38.580748 110 0 0 32.849694 38.574221 111 0 0 32.818396 38.54803 112 0 0 32.755798 38.496649 113 0 0 32.70426 38.458252 114 0 0 32.656388 38.418404 115 0 0 32.611595 38.381267 116 0 0 32.557308 38.33692 117 0 0 32.552944 38.337957 118 0 0 32.548604 38.337699 119 0 0 32.541358 38.332992 120 0 0 32.553519 38.341425 121 0 0 32.55042 38.339813 122 0 0 32.577985 38.359077 123 0 0 32.593111 38.370727 124 0 0 32.618919 38.388102 125 0 0 32.634364 38.400201 126 0 0 32.659722 38.414308 127 0 0 32.648923 38.398629 128 0 0 32.648139 38.396151 129 0 0 32.640383 38.386927 130 0 0 32.612179 38.363547 131 0 0 32.593601 38.348788 132 0 0 32.578619 38.336256 133 0 0 32.575695 38.32988 134 0 0 32.584261 38.340242 135 0 0 32.567202 38.320742 136 0 0 32.55428 38.313646 137 0 0 32.548716 38.309636 138 0 0 32.548495 38.308112 139 0 0 32.574623 38.332421 140 0 0 32.587016 38.341701 141 0 0 32.622544 38.373198 142 0 0 32.635277 38.380057 143 0 0 32.653509 38.394951 144 0 0 32.653873 38.393563 145 0 0 32.648798 38.38771 146 0 0 32.618856 38.356304 147 0 0 32.591387 38.3352 148 0 0 32.563846 38.309397 149 0 0 32.520439 38.269603 150 0 0 32.483378 38.241553 151 0 0 32.482849 38.241144 152 0 0 32.427486 38.200623 153 0 0 32.417077 38.190821 154 0 0 32.435568 38.209725 155 0 0 32.41938 38.192213 156 0 0 32.432684 38.202968 157 0 0 32.451273 38.216002 158 0 0 32.490509 38.245529 159 0 0 32.538313 38.284285 160 0 0 32.547345 38.292234 161 0 0 32.583488 38.321194 162 0 0 32.628097 38.354453 163 0 0 32.649669 38.378415 164 0 0 32.677294 38.39328 165 0 0 32.672979 38.388699 166 0 0 32.687494 38.400349 167 0 0 32.644324 38.360252 168 0 0 32.625249 38.336806 169 0 0 32.573063 38.302947 170 0 0 32.577874 38.298932 171 0 0 32.54408 38.269829 172 0 0 32.524134 38.256165 173 0 0 32.524633 38.261317 174 0 0 32.528492 38.26009 175 0 0 32.571269 38.298298 176 0 0 32.573811 38.304708 177 0 0 32.616007 38.338468 178 0 0 32.674815 38.387406 179 0 0 32.66911 38.383699 180 0 0 32.746598 38.449629 181 0 0 32.772405 38.47434 182 0 0 32.817772 38.510593 183 0 0 32.852986 38.542751 184 0 0 32.908807 38.58415 185 0 0 32.936367 38.604417 186 0 0 32.966631 38.632149 187 0 0 32.989688 38.651228 188 0 0 32.993732 38.653235 189 0 0 32.982735 38.6434 190 0 0 32.985957 38.65411 191 0 0 32.979998 38.650907 192 0 0 32.961507 38.64031 193 0 0 32.936657 38.629613 194 0 0 32.910125 38.606339 195 0 0 32.929007 38.622359 196 0 0 32.915306 38.6185 197 0 0 32.883272 38.601893 198 0 0 32.892352 38.612975 199 0 0 32.883306 38.61609 200 0 0 32.858336 38.609242 201 0 0 32.890317 38.644876 202 0 0 32.853733 38.615567 203 0 0 32.879698 38.644334 204 0 0 32.852542 38.618948 205 0 0 32.8503 38.631624 206 0 0 32.820839 38.621715 207 0 0 32.804234 38.602346 208 0 0 32.775963 38.5876 209 0 0 32.727074 38.552287 210 0 0 32.745267 38.583402 211 0 0 32.749408 38.586378 212 0 0 32.76002 38.602101 213 0 0 32.740486 38.587343 214 0 0 32.681597 38.538148 215 0 0 32.668347 38.541826 216 0 0 32.61315 38.489747 217 0 0 32.607947 38.489772 218 0 0 32.521665 38.431197 219 0 0 32.559755 38.46652 220 0 0 32.59 38.49126 221 0 0 32.428156 38.391298 222 0 0 32.529968 38.451844 223 0 0 32.541426 38.452414 224 0 0 32.482242 38.424903 225 0 0 32.483397 38.431316 226 0 0 32.38246 38.370482 227 0 0 32.341368 38.350365 228 0 0 32.387604 38.390111 229 0 0 32.397642 38.387435 230 0 0 32.260432 38.294291 231 0 0 32.324372 38.331285 232 0 0 32.287367 38.323669 233 0 0 32.252299 38.267056 234 0 0 32.247319 38.283 235 0 0 32.265339 38.308386 236 0 0 32.143128 38.208101 237 0 0 32.141504 38.217731 238 0 0 32.087378 38.185308 239 0 0 32.143756 38.24215 240 0 0 32.052834 38.15113 241 0 0 32.099084 38.204106 242 0 0 32.063928 38.176836 243 0 0 31.943702 38.084218 244 0 0 31.881498 38.046711 245 0 0 31.829651 38.007193 246 0 0 31.936185 38.103709 247 0 0 31.803217 38.007054 248 0 0 31.728713 37.968026 249 0 0 31.758712 38.004856 250 0 0 31.680184 37.94738 251 0 0 31.675301 37.951035 252 0 0 31.680058 37.926529 253 0 0 31.480982 37.798289 254 0 0 31.641868 37.917709 255 0 0 31.578007 37.866732 256 0 0 31.393869 37.746261 257 0 0 31.497514 37.813204 258 0 0 31.47443 37.811954 259 0 0 31.427263 37.788659 260 0 0 31.453142 37.804257 261 0 0 31.288037 37.672353 262 0 0 31.02065 37.452266 263 0 0 31.148834 37.579667 264 0 0 31.012039 37.478993 265 0 0 31.073934 37.538874 266 0 0 31.090745 37.562878 267 0 0 30.98723 37.493637 268 0 0 31.04792 37.534033 269 0 0 30.976453 37.491095 270 0 0 30.831907 37.424162 271 0 0 30.706978 37.27172 272 0 0 30.725022 37.353843 273 0 0 30.60231 37.230523 274 0 0 30.424586 37.143368 275 0 0 30.520325 37.149156 276 0 0 30.191439 36.962869 277 0 0 30.060912 36.880836 278 0 0 30.191589 36.943425 279 0 0 30.133607 36.920895 280 0 0 29.916374 36.788336 281 0 0 29.876331 36.729253 282 0 0 29.652399 36.574331 283 0 0 29.756079 36.67273 284 0 0 29.760887 36.684877 285 0 0 29.687244 36.608012 286 0 0 29.545955 36.553791 287 0 0 29.531381 36.531601 288 0 0 29.444521 36.442618 289 0 0 29.328103 36.392059 290 0 0 29.591427 36.54369 291 0 0 29.334365 36.358273 292 0 0 29.244014 36.229307 293 0 0 29.228821 36.298058 294 0 0 29.15101 36.157643 295 0 0 29.127582 36.225597 296 0 0 29.166826 36.28134 297 0 0 29.086519 36.200313 298 0 0 28.737249 35.984054 299 0 0 28.487426 35.853797 300 0 0 29.101938 36.224935 301 0 0 28.99024 36.19249 302 0 0 28.767911 35.924782 303 0 0 29.082284 36.176259 304 0 0 29.01526 36.127007 305 0 0 28.335693 35.749747 306 0 0 28.494873 35.767944 307 0 0 28.238257 35.650066 308 0 0 28.091511 35.481638 309 0 0 28.373479 35.746957 310 0 0 28.71564 35.930715 311 0 0 28.389706 35.808824 312 0 0 27.925456 35.405234 313 0 0 27.97708 35.423033 314 0 0 27.918107 35.398241 315 0 0 28.421569 35.72451 316 0 0 28.061571 35.548478 317 0 0 27.831981 35.26265 318 0 0 28.299371 35.657023 319 0 0 27.27628 34.867925 320 0 0 27.757971 35.25942 321 0 0 28.006421 35.326378 322 0 0 27.53169 34.998239 323 0 0 27.375723 35.104046 324 0 0 28.153509 35.438596 325 0 0 27.950355 35.497242 326 0 0 27.889175 35.21134 327 0 0 27.953757 35.364162 328 0 0 28.485893 35.713689 329 0 0 27.358696 34.788647 330 0 0 28.27686 35.559229 331 0 0 28.377273 35.392424 332 0 0 28.268293 35.905691 333 0 0 27.325714 34.84 334 0 0 27.205298 34.613687 335 0 0 27.720588 34.995098 336 0 0 27.543307 35.165354 337 0 0 27.452174 35.150725 338 0 0 27.613861 35.19802 339 0 0 27.579545 35.170455 340 0 0 27.230769 34.970085 341 0 0 27.169014 34.967136 342 0 0 27.65 35.25 343 0 0 28.981818 36.448485 344 0 0 24.634146 32.707317 345 0 0 28 35.380952 346 0 0 25.148148 33.049383 347 0 0 26.541667 34.444444 348 0 0 28.684211 34.596491 349 0 0 27.625 35.270833 350 0 0 26.461538 34.769231 351 0 0 24.727273 33.484848 352 0 0 23.7 32.9 353 0 0 31.714286 38.238095 354 0 0 32.6 39.2 355 0 0 23.75 32.666667 356 0 0 26.333333 33.888889 357 0 0 20 27.666667 358 0 0 24.5 32.166667 359 0 0 34.5 39.333333 360 0 0 35.5 40.333333 361 0 0 35 40 362 0 0 33 37.666667 363 0 0 26 36 364 0 0 36 41 365 0 0 36 41