## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5400-Z0089-CTGCTACAAGCAGAT/441525-L5400-Z0089-CTGCTACAAGCAGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5400-Z0089-CTGCTACAAGCAGAT/441525-L5400-Z0089-CTGCTACAAGCAGAT_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 02:59:56 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 1000717 1000717 124 124704654 124704654 119475632 119475632 110189466 110189466 0 0 0.958069 0.883603 0 0.958069 0.883603 0 374113962 374113962 367182050 367182050 352057253 352057253 327368412 327368412 0.981471 0.941043 0.87505 0.981471 0.941043 0.87505 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 1022 0 35.994212 40.995694 1 13379 1 35.988116 40.991962 2 15262 5215 35.995074 40.995913 3 40159 1367 35.983332 40.986107 4 61451 57210 35.990762 40.992125 5 126989 21174 35.995821 40.996629 6 115889 145230 35.98313 40.986241 7 219023 182576 35.976783 40.983493 8 201715 159066 35.98853 40.990261 9 262282 128609 35.963147 40.969062 10 277641 530735 35.889139 40.934334 11 326834 71654 35.917003 40.938857 12 383629 760906 35.20775 40.329205 13 372536 227734 33.553846 39.485804 14 497162 1068826 35.894238 40.936347 15 397185 406902 35.810789 40.865725 16 412230 469179 35.776236 40.798449 17 538933 1172412 35.887457 40.902605 18 582007 792060 35.673445 40.734743 19 383694 731056 35.665604 40.747827 20 529820 1019055 35.876079 40.912218 21 690699 1460234 35.682181 40.743914 22 333946 566749 35.371806 40.541103 23 1081729 1270966 34.596141 39.851996 24 602064 1268300 34.891027 40.154603 25 541721 481270 35.14477 40.389815 26 1757718 2610492 34.89759 40.15433 27 390915 918644 34.990958 40.292194 28 945972 405165 34.935427 40.275996 29 2411582 5123922 34.863701 40.206218 30 765996 39232 35.092615 40.369233 31 2296368 830557 35.09577 40.368819 32 1630078 5475913 34.97694 40.253463 33 829724 131561 35.081074 40.351872 34 2413281 2673176 35.145183 40.412265 35 2186008 3829993 35.16914 40.430781 36 100068011 2167516 35.18921 40.444197 37 0 4223368 35.19865 40.452597 38 0 364363 35.183697 40.442677 39 0 4953162 35.183355 40.439807 40 0 1 35.128653 40.401094 41 0 327368411 35.139418 40.404051 42 0 0 35.124237 40.396691 43 0 0 35.12647 40.400173 44 0 0 35.111578 40.384813 45 0 0 35.100292 40.371917 46 0 0 35.09516 40.367645 47 0 0 35.072977 40.349654 48 0 0 34.990531 40.295235 49 0 0 34.998983 40.302235 50 0 0 35.058549 40.345973 51 0 0 35.074976 40.357617 52 0 0 34.803521 40.163379 53 0 0 34.561024 40.019158 54 0 0 34.623985 40.034963 55 0 0 34.540902 39.970252 56 0 0 34.266417 39.801277 57 0 0 34.617615 40.024562 58 0 0 34.616471 40.001816 59 0 0 34.442869 39.862348 60 0 0 34.454817 39.941477 61 0 0 34.428212 39.91118 62 0 0 34.428466 39.888736 63 0 0 34.47426 39.909571 64 0 0 34.380537 39.838792 65 0 0 34.294385 39.777183 66 0 0 34.307428 39.793984 67 0 0 34.345794 39.817863 68 0 0 34.264912 39.759459 69 0 0 34.179707 39.693007 70 0 0 34.05998 39.601301 71 0 0 33.93002 39.495912 72 0 0 33.776626 39.374051 73 0 0 33.618357 39.243525 74 0 0 33.485685 39.13109 75 0 0 33.366252 39.040075 76 0 0 33.234088 38.939334 77 0 0 33.105006 38.843269 78 0 0 32.966554 38.736168 79 0 0 32.807225 38.609932 80 0 0 32.629085 38.478327 81 0 0 32.580528 38.450661 82 0 0 32.626855 38.476452 83 0 0 32.632327 38.466224 84 0 0 32.595459 38.436547 85 0 0 32.561881 38.406547 86 0 0 32.527516 38.376907 87 0 0 32.48307 38.340771 88 0 0 32.455228 38.315372 89 0 0 32.396606 38.263128 90 0 0 32.36214 38.230584 91 0 0 32.323974 38.193069 92 0 0 32.276131 38.150104 93 0 0 32.239272 38.123053 94 0 0 32.204622 38.089868 95 0 0 32.170743 38.060214 96 0 0 32.150732 38.045208 97 0 0 32.12203 38.022899 98 0 0 32.140366 38.037499 99 0 0 32.150686 38.045388 100 0 0 32.179373 38.065748 101 0 0 32.229964 38.107388 102 0 0 32.279057 38.144614 103 0 0 32.325708 38.175326 104 0 0 32.382703 38.213992 105 0 0 32.409747 38.234891 106 0 0 32.420245 38.239517 107 0 0 32.452035 38.264078 108 0 0 32.465873 38.277678 109 0 0 32.465647 38.27527 110 0 0 32.461745 38.272726 111 0 0 32.440049 38.255947 112 0 0 32.383507 38.206194 113 0 0 32.343732 38.174664 114 0 0 32.303163 38.139045 115 0 0 32.277301 38.117992 116 0 0 32.241261 38.091267 117 0 0 32.219707 38.081444 118 0 0 32.209241 38.077923 119 0 0 32.256327 38.114794 120 0 0 32.284337 38.138586 121 0 0 32.290265 38.139514 122 0 0 32.328039 38.170228 123 0 0 32.349057 38.182553 124 0 0 32.392094 38.216105 125 0 0 32.434497 38.245765 126 0 0 32.473503 38.273002 127 0 0 32.487563 38.278849 128 0 0 32.496874 38.282668 129 0 0 32.510911 38.288831 130 0 0 32.496918 38.282921 131 0 0 32.492749 38.275689 132 0 0 32.498224 38.276473 133 0 0 32.504201 38.282118 134 0 0 32.508282 38.282257 135 0 0 32.528846 38.296988 136 0 0 32.515295 38.27977 137 0 0 32.521433 38.287719 138 0 0 32.508089 38.282907 139 0 0 32.520673 38.293482 140 0 0 32.595887 38.353634 141 0 0 32.621708 38.374684 142 0 0 32.644859 38.387818 143 0 0 32.650642 38.393376 144 0 0 32.664499 38.400911 145 0 0 32.644326 38.386247 146 0 0 32.637822 38.379073 147 0 0 32.634566 38.37138 148 0 0 32.611286 38.354287 149 0 0 32.582327 38.328253 150 0 0 32.588925 38.332419 151 0 0 32.560779 38.314169 152 0 0 32.529371 38.285382 153 0 0 32.545394 38.295704 154 0 0 32.549425 38.299636 155 0 0 32.572283 38.318861 156 0 0 32.592407 38.3307 157 0 0 32.597236 38.339488 158 0 0 32.621536 38.351653 159 0 0 32.675742 38.399534 160 0 0 32.684046 38.401709 161 0 0 32.73743 38.445553 162 0 0 32.752853 38.454979 163 0 0 32.795808 38.493454 164 0 0 32.827581 38.51594 165 0 0 32.834771 38.522882 166 0 0 32.83259 38.517391 167 0 0 32.840751 38.518841 168 0 0 32.791598 38.476489 169 0 0 32.762173 38.450007 170 0 0 32.739462 38.425124 171 0 0 32.704942 38.399496 172 0 0 32.715352 38.412443 173 0 0 32.739299 38.429328 174 0 0 32.725094 38.419558 175 0 0 32.741371 38.438937 176 0 0 32.779014 38.474757 177 0 0 32.776897 38.467211 178 0 0 32.822051 38.506783 179 0 0 32.87365 38.549039 180 0 0 32.885497 38.556843 181 0 0 32.938691 38.605907 182 0 0 32.95539 38.61518 183 0 0 33.032222 38.682764 184 0 0 33.07017 38.713002 185 0 0 33.090978 38.729361 186 0 0 33.128925 38.757505 187 0 0 33.142251 38.770897 188 0 0 33.16736 38.789298 189 0 0 33.191647 38.811449 190 0 0 33.190026 38.806843 191 0 0 33.173332 38.798988 192 0 0 33.141204 38.783071 193 0 0 33.146392 38.77889 194 0 0 33.164888 38.815073 195 0 0 33.065376 38.741151 196 0 0 33.13213 38.796477 197 0 0 33.13716 38.807086 198 0 0 33.080421 38.771275 199 0 0 33.056551 38.7596 200 0 0 33.040652 38.747375 201 0 0 33.101143 38.806973 202 0 0 33.029676 38.755064 203 0 0 33.009284 38.746396 204 0 0 33.008939 38.755986 205 0 0 32.983567 38.747494 206 0 0 32.917636 38.700396 207 0 0 32.944312 38.721412 208 0 0 32.897044 38.687558 209 0 0 32.93392 38.724952 210 0 0 32.872144 38.681175 211 0 0 32.831191 38.658056 212 0 0 32.83129 38.657054 213 0 0 32.799668 38.649185 214 0 0 32.802666 38.64785 215 0 0 32.767136 38.62797 216 0 0 32.773112 38.623512 217 0 0 32.711238 38.596819 218 0 0 32.778127 38.645079 219 0 0 32.743169 38.598765 220 0 0 32.721108 38.595684 221 0 0 32.693833 38.579749 222 0 0 32.718398 38.612209 223 0 0 32.683484 38.57461 224 0 0 32.611587 38.524284 225 0 0 32.624625 38.556261 226 0 0 32.583971 38.511835 227 0 0 32.621438 38.545945 228 0 0 32.521829 38.465703 229 0 0 32.549958 38.498532 230 0 0 32.544628 38.48772 231 0 0 32.478683 38.463879 232 0 0 32.489797 38.458192 233 0 0 32.414942 38.417058 234 0 0 32.458109 38.453249 235 0 0 32.420061 38.445998 236 0 0 32.367286 38.37495 237 0 0 32.393001 38.419371 238 0 0 32.27164 38.318508 239 0 0 32.261737 38.31008 240 0 0 32.2238 38.287911 241 0 0 32.248496 38.317497 242 0 0 32.239863 38.291993 243 0 0 32.197829 38.292065 244 0 0 32.22165 38.304591 245 0 0 32.247477 38.31307 246 0 0 32.089742 38.229983 247 0 0 32.118977 38.25762 248 0 0 32.146816 38.276421 249 0 0 31.986482 38.184055 250 0 0 31.993038 38.163498 251 0 0 31.921004 38.108179 252 0 0 31.760666 38.034182 253 0 0 31.865532 38.074931 254 0 0 31.842627 38.05476 255 0 0 31.738759 37.994101 256 0 0 31.661972 37.916905 257 0 0 31.763341 37.995753 258 0 0 31.754734 38.017703 259 0 0 31.608631 37.930955 260 0 0 31.625945 37.900008 261 0 0 31.574855 37.879661 262 0 0 31.50062 37.826224 263 0 0 31.531008 37.88476 264 0 0 31.264438 37.671089 265 0 0 31.395758 37.794718 266 0 0 31.279945 37.733288 267 0 0 31.269915 37.693919 268 0 0 31.390632 37.781263 269 0 0 31.265417 37.70812 270 0 0 31.27488 37.671813 271 0 0 31.070696 37.588064 272 0 0 31.053809 37.577455 273 0 0 31.01552 37.550187 274 0 0 30.793312 37.380805 275 0 0 30.86898 37.42937 276 0 0 30.751568 37.339378 277 0 0 30.801074 37.368163 278 0 0 30.573076 37.224016 279 0 0 30.463432 37.117789 280 0 0 30.315003 37.021529 281 0 0 30.409787 37.089174 282 0 0 30.202206 36.98652 283 0 0 30.30609 37.049197 284 0 0 29.909626 36.765638 285 0 0 30.199958 36.992966 286 0 0 30.146567 36.931974 287 0 0 30.084194 36.912508 288 0 0 29.920354 36.801301 289 0 0 29.924533 36.829206 290 0 0 29.887175 36.749759 291 0 0 29.79717 36.71905 292 0 0 29.723311 36.661595 293 0 0 29.512663 36.52777 294 0 0 29.488053 36.502884 295 0 0 29.570779 36.510138 296 0 0 29.41208 36.443519 297 0 0 29.359554 36.427377 298 0 0 29.194877 36.242434 299 0 0 29.002384 36.195618 300 0 0 29.275229 36.352152 301 0 0 29.402299 36.478556 302 0 0 29.03876 36.198966 303 0 0 28.98292 36.179341 304 0 0 29.049871 36.227142 305 0 0 28.622951 35.882514 306 0 0 29.103365 36.1875 307 0 0 29.050228 36.147472 308 0 0 28.680631 35.891186 309 0 0 28.821719 36.019164 310 0 0 28.304644 35.606605 311 0 0 28.899467 36.092321 312 0 0 28.259049 35.64159 313 0 0 28.65367 35.909531 314 0 0 28.406302 35.749585 315 0 0 28.47861 35.733512 316 0 0 28.45821 35.76434 317 0 0 28.938034 36.064103 318 0 0 27.849825 35.287544 319 0 0 28.54023 35.747552 320 0 0 28.832861 35.902738 321 0 0 28.677621 35.742306 322 0 0 28.760417 35.978009 323 0 0 28.593928 35.800127 324 0 0 27.87234 35.455319 325 0 0 28.273171 35.652033 326 0 0 28.292553 35.745567 327 0 0 28.889881 35.944444 328 0 0 27.867742 35.268817 329 0 0 28.039855 35.644928 330 0 0 27.139344 34.845628 331 0 0 27.656388 35.20558 332 0 0 27.571429 35.305419 333 0 0 29.551136 36.511364 334 0 0 27.324841 34.704883 335 0 0 28.211679 35.715328 336 0 0 27.284553 34.98374 337 0 0 27.7 34.906061 338 0 0 28.505051 35.538721 339 0 0 28.146067 35.337079 340 0 0 27.54878 34.914634 341 0 0 26.906667 34.497778 342 0 0 30.123077 36.646154 343 0 0 27.145455 35.230303 344 0 0 28.369565 36.217391 345 0 0 26.714286 34.47619 346 0 0 29.171429 36.695238 347 0 0 27.851852 36.074074 348 0 0 25.64 33.88 349 0 0 30.347826 37 350 0 0 28.529412 35.54902 351 0 0 28.461538 35.410256 352 0 0 25.166667 34.194444 353 0 0 31.4 38.333333 354 0 0 30.888889 37.703704 355 0 0 34.571429 40 356 0 0 22.714286 31.095238 357 0 0 32 38.285714 358 0 0 28 35.238095 359 0 0 25.6 32.066667 360 0 0 36 41 361 0 0 17.5 31.833333 362 0 0 21.5 35.333333 363 0 0 18.5 31 364 0 0 27 34.166667 365 0 0 36 41 366 0 0 13 25.5 367 0 0 30.5 36.333333 368 0 0 25.5 33.333333 369 0 0 26.5 35 370 0 0 33 38 371 0 0 16.5 26.5 372 0 0 32 38.666667 373 0 0 36 41 374 0 0 36 41 375 0 0 26 36.333333 376 0 0 5 23.333333