## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5389-Z0075-CTATGCACCATCGAT/441525-L5389-Z0075-CTATGCACCATCGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5389-Z0075-CTATGCACCATCGAT/441525-L5389-Z0075-CTATGCACCATCGAT_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 02:54:34 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 999383 999383 136 136256649 136256649 131601381 131601381 122416565 122416565 0 0 0.965835 0.898426 0 0.965835 0.898426 0 408769947 408769947 402598251 402598251 388089579 388089579 362960294 362960294 0.984902 0.949408 0.887933 0.984902 0.949408 0.887933 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 810 0 35.98852 40.991719 1 10019 0 35.978352 40.985523 2 12491 4121 35.993592 40.994761 3 31576 1118 35.96658 40.973622 4 52534 42937 35.985575 40.988329 5 101787 14869 35.992875 40.993947 6 108834 113588 35.966572 40.972455 7 184371 146821 35.973588 40.982019 8 190442 141799 35.985194 40.987898 9 229690 97965 35.932776 40.942856 10 236516 499409 35.814386 40.884659 11 279068 55233 35.888142 40.918432 12 326821 684106 35.189702 40.325907 13 337105 192863 33.689906 39.568331 14 427467 947278 35.835584 40.899347 15 355486 347502 35.779412 40.84424 16 366778 429239 35.707852 40.743451 17 502512 1068682 35.859241 40.8808 18 526056 693642 35.629771 40.694601 19 374905 690524 35.660445 40.737813 20 497195 983639 35.881534 40.91754 21 641516 1327956 35.810178 40.860963 22 323217 549557 35.576491 40.714065 23 1024694 1206693 35.23559 40.455675 24 570568 1155481 35.324554 40.541692 25 543282 484116 35.348874 40.559359 26 1762526 2462558 35.266729 40.489704 27 355159 879112 35.299962 40.526861 28 965716 389598 35.299968 40.5276 29 2500943 5069962 35.296111 40.521186 30 803988 41532 35.334176 40.548836 31 2411327 833404 35.33233 40.543789 32 1622731 5499224 35.30704 40.521813 33 874639 123766 35.338343 40.549314 34 2528828 2692331 35.331933 40.54579 35 2304685 3935313 35.345719 40.555543 36 111870367 2058633 35.369026 40.571933 37 0 4386324 35.374679 40.577194 38 0 395541 35.365043 40.571714 39 0 5163217 35.364007 40.56915 40 0 2 35.352296 40.560479 41 0 362960292 35.350734 40.558294 42 0 0 35.339957 40.552738 43 0 0 35.345945 40.554781 44 0 0 35.348701 40.558803 45 0 0 35.353958 40.561515 46 0 0 35.347511 40.55565 47 0 0 35.331904 40.544033 48 0 0 35.305507 40.52652 49 0 0 35.314121 40.531514 50 0 0 35.32697 40.542163 51 0 0 35.315514 40.533785 52 0 0 35.27631 40.507949 53 0 0 35.255419 40.502821 54 0 0 35.267049 40.506631 55 0 0 35.260834 40.501664 56 0 0 35.219448 40.484735 57 0 0 35.270349 40.504846 58 0 0 35.256358 40.492136 59 0 0 35.234526 40.475441 60 0 0 35.210962 40.458311 61 0 0 35.184624 40.439554 62 0 0 35.149663 40.413605 63 0 0 35.112393 40.386072 64 0 0 35.074789 40.355488 65 0 0 35.029204 40.32451 66 0 0 34.980199 40.286775 67 0 0 34.92123 40.244495 68 0 0 34.868273 40.203177 69 0 0 34.786333 40.14373 70 0 0 34.710928 40.08327 71 0 0 34.616618 40.009932 72 0 0 34.52335 39.935333 73 0 0 34.436399 39.865737 74 0 0 34.340162 39.78747 75 0 0 34.238184 39.707495 76 0 0 34.147163 39.637488 77 0 0 34.048113 39.561715 78 0 0 33.956008 39.492029 79 0 0 33.865652 39.421009 80 0 0 33.782427 39.350488 81 0 0 33.698611 39.285637 82 0 0 33.623741 39.22186 83 0 0 33.547903 39.162064 84 0 0 33.491799 39.118647 85 0 0 33.430154 39.066967 86 0 0 33.387237 39.032865 87 0 0 33.331141 38.986525 88 0 0 33.26875 38.932766 89 0 0 33.229635 38.901646 90 0 0 33.167643 38.845698 91 0 0 33.126187 38.808615 92 0 0 33.078761 38.767897 93 0 0 33.043684 38.736446 94 0 0 33.012759 38.710745 95 0 0 32.998268 38.697189 96 0 0 32.97295 38.674167 97 0 0 32.959551 38.661402 98 0 0 32.969283 38.669239 99 0 0 32.99221 38.686966 100 0 0 33.013629 38.7023 101 0 0 33.048938 38.72955 102 0 0 33.083466 38.755376 103 0 0 33.105563 38.770849 104 0 0 33.116508 38.780485 105 0 0 33.131086 38.783247 106 0 0 33.128631 38.782263 107 0 0 33.114699 38.768954 108 0 0 33.088555 38.748889 109 0 0 33.084824 38.743538 110 0 0 33.040223 38.711315 111 0 0 32.982749 38.665227 112 0 0 32.934757 38.626112 113 0 0 32.868851 38.568909 114 0 0 32.811798 38.524791 115 0 0 32.74943 38.473428 116 0 0 32.708248 38.443295 117 0 0 32.694567 38.435528 118 0 0 32.677083 38.423552 119 0 0 32.678869 38.426923 120 0 0 32.688626 38.435367 121 0 0 32.688078 38.432973 122 0 0 32.692502 38.437781 123 0 0 32.70412 38.4418 124 0 0 32.713855 38.448872 125 0 0 32.721192 38.453207 126 0 0 32.725189 38.449391 127 0 0 32.734508 38.45022 128 0 0 32.71643 38.434389 129 0 0 32.676112 38.401095 130 0 0 32.66314 38.389321 131 0 0 32.629786 38.36362 132 0 0 32.60351 38.342557 133 0 0 32.614847 38.351297 134 0 0 32.605788 38.343203 135 0 0 32.595646 38.330621 136 0 0 32.589104 38.325037 137 0 0 32.59647 38.330379 138 0 0 32.582105 38.319713 139 0 0 32.596207 38.332959 140 0 0 32.621398 38.357525 141 0 0 32.645524 38.374355 142 0 0 32.662098 38.38658 143 0 0 32.666908 38.390386 144 0 0 32.646686 38.374529 145 0 0 32.616337 38.345351 146 0 0 32.616544 38.341932 147 0 0 32.570612 38.301064 148 0 0 32.513753 38.256304 149 0 0 32.512523 38.255745 150 0 0 32.462102 38.213932 151 0 0 32.428133 38.185491 152 0 0 32.407525 38.171416 153 0 0 32.38181 38.151791 154 0 0 32.392072 38.160099 155 0 0 32.385986 38.153292 156 0 0 32.408326 38.175487 157 0 0 32.416811 38.177683 158 0 0 32.462382 38.215207 159 0 0 32.52405 38.258843 160 0 0 32.535508 38.271167 161 0 0 32.55907 38.290998 162 0 0 32.602149 38.322038 163 0 0 32.628856 38.343811 164 0 0 32.647716 38.361494 165 0 0 32.654068 38.365775 166 0 0 32.651415 38.359754 167 0 0 32.615364 38.333001 168 0 0 32.590069 38.298802 169 0 0 32.552063 38.272855 170 0 0 32.535539 38.259122 171 0 0 32.517388 38.239857 172 0 0 32.501923 38.230896 173 0 0 32.531582 38.259965 174 0 0 32.529622 38.256672 175 0 0 32.554719 38.282445 176 0 0 32.577479 38.297155 177 0 0 32.601223 38.325606 178 0 0 32.668 38.374131 179 0 0 32.678088 38.386953 180 0 0 32.73909 38.437311 181 0 0 32.809485 38.499994 182 0 0 32.824912 38.513906 183 0 0 32.881881 38.552698 184 0 0 32.896501 38.574301 185 0 0 32.971903 38.641509 186 0 0 32.969971 38.632647 187 0 0 33.006472 38.665365 188 0 0 33.016097 38.666403 189 0 0 33.05272 38.701754 190 0 0 33.029744 38.689095 191 0 0 33.013868 38.671572 192 0 0 33.014673 38.685248 193 0 0 32.958659 38.647146 194 0 0 32.950013 38.634659 195 0 0 32.981753 38.669023 196 0 0 32.935772 38.638254 197 0 0 32.910367 38.626949 198 0 0 32.923346 38.641989 199 0 0 32.868052 38.610022 200 0 0 32.904578 38.643565 201 0 0 32.8872 38.64272 202 0 0 32.882636 38.642766 203 0 0 32.840872 38.628647 204 0 0 32.82587 38.617212 205 0 0 32.810534 38.606386 206 0 0 32.786446 38.597668 207 0 0 32.78538 38.604257 208 0 0 32.805099 38.61713 209 0 0 32.802825 38.624266 210 0 0 32.723913 38.557183 211 0 0 32.728529 38.57088 212 0 0 32.671711 38.539341 213 0 0 32.614824 38.503116 214 0 0 32.651979 38.520585 215 0 0 32.584496 38.47864 216 0 0 32.571789 38.47851 217 0 0 32.520072 38.439615 218 0 0 32.488232 38.430173 219 0 0 32.489277 38.427408 220 0 0 32.469033 38.408526 221 0 0 32.404273 38.371561 222 0 0 32.448713 38.407931 223 0 0 32.366741 38.339827 224 0 0 32.397361 38.370784 225 0 0 32.386259 38.358896 226 0 0 32.365118 38.345186 227 0 0 32.348784 38.331477 228 0 0 32.351122 38.351049 229 0 0 32.360597 38.355168 230 0 0 32.306305 38.322095 231 0 0 32.3473 38.344086 232 0 0 32.203599 38.245658 233 0 0 32.298923 38.311255 234 0 0 32.275354 38.30671 235 0 0 32.124382 38.200955 236 0 0 32.122209 38.201142 237 0 0 32.17867 38.252205 238 0 0 32.079077 38.18532 239 0 0 32.054509 38.149389 240 0 0 32.058088 38.169962 241 0 0 31.929221 38.08357 242 0 0 31.918199 38.074788 243 0 0 31.88574 38.050205 244 0 0 31.90388 38.072051 245 0 0 31.854761 38.023467 246 0 0 31.89647 38.056291 247 0 0 31.783625 37.962493 248 0 0 31.781273 37.994199 249 0 0 31.634167 37.883519 250 0 0 31.627512 37.864632 251 0 0 31.71257 37.973279 252 0 0 31.550263 37.808761 253 0 0 31.724293 37.971276 254 0 0 31.56956 37.862967 255 0 0 31.581075 37.892728 256 0 0 31.479522 37.772905 257 0 0 31.390485 37.731569 258 0 0 31.264042 37.638092 259 0 0 31.486879 37.805661 260 0 0 31.257424 37.655514 261 0 0 31.391964 37.745742 262 0 0 31.315595 37.69471 263 0 0 31.151124 37.607537 264 0 0 31.227227 37.598912 265 0 0 31.068526 37.571591 266 0 0 30.902769 37.398864 267 0 0 31.128846 37.620959 268 0 0 30.954306 37.471641 269 0 0 30.779035 37.344051 270 0 0 30.666275 37.247359 271 0 0 30.618762 37.224547 272 0 0 30.62155 37.265483 273 0 0 30.631096 37.26879 274 0 0 30.458188 37.166514 275 0 0 30.36757 37.064459 276 0 0 30.198728 36.930159 277 0 0 30.515403 37.198657 278 0 0 30.273537 37.005804 279 0 0 30.315003 37.023933 280 0 0 30.054037 36.857738 281 0 0 30.066464 36.869244 282 0 0 29.895736 36.730371 283 0 0 29.911192 36.794919 284 0 0 29.884962 36.701929 285 0 0 29.741935 36.625122 286 0 0 29.618196 36.59879 287 0 0 29.674316 36.615906 288 0 0 29.619163 36.546289 289 0 0 29.365745 36.347956 290 0 0 29.352051 36.342741 291 0 0 29.472567 36.48449 292 0 0 29.427804 36.367983 293 0 0 29.495419 36.480585 294 0 0 29.338655 36.368093 295 0 0 29.34523 36.404122 296 0 0 29.097902 36.229174 297 0 0 29.24489 36.286926 298 0 0 28.971717 36.057374 299 0 0 28.7173 35.906892 300 0 0 28.920656 36.12633 301 0 0 28.750467 36.056075 302 0 0 28.847168 36.023763 303 0 0 28.723996 35.952798 304 0 0 28.385614 35.723454 305 0 0 28.641011 35.914226 306 0 0 28.203995 35.528652 307 0 0 28.174522 35.49448 308 0 0 28.682249 35.866531 309 0 0 28.714699 35.982621 310 0 0 28.615444 35.849163 311 0 0 28.41742 35.711038 312 0 0 28.253369 35.695118 313 0 0 28.286957 35.672142 314 0 0 27.990516 35.358623 315 0 0 27.774857 35.371048 316 0 0 28.365915 35.767335 317 0 0 28.037787 35.440846 318 0 0 28.320644 35.736945 319 0 0 27.855987 35.452535 320 0 0 27.841637 35.39917 321 0 0 28.568627 35.905882 322 0 0 27.884026 35.391685 323 0 0 27.257212 34.957532 324 0 0 27.268293 35.118338 325 0 0 27.355224 35.130348 326 0 0 26.694805 34.901515 327 0 0 27.700348 35.235772 328 0 0 28.329412 35.743791 329 0 0 27.821429 35.160714 330 0 0 27.20202 34.794613 331 0 0 28.61236 35.677903 332 0 0 26.895062 34.557613 333 0 0 27.326389 34.983796 334 0 0 28.206349 35.531746 335 0 0 28.663793 35.804598 336 0 0 28.958333 35.996528 337 0 0 27.111111 34.785185 338 0 0 28.098765 35.316872 339 0 0 27.328358 34.920398 340 0 0 29.644068 36.508475 341 0 0 26.730769 34.730769 342 0 0 28.465116 36.031008 343 0 0 29.75 36.866667 344 0 0 24.515152 33.454545 345 0 0 28.633333 36.322222 346 0 0 29.392857 36.511905 347 0 0 28.909091 36.136364 348 0 0 25.45 33 349 0 0 23.85 32.616667 350 0 0 23.8 32.955556 351 0 0 24.230769 32.589744 352 0 0 25.181818 34.121212 353 0 0 25.3 33.5 354 0 0 24 33.875 355 0 0 31.666667 37.166667 356 0 0 29.4 35.866667 357 0 0 25.5 34.416667 358 0 0 24.333333 33.222222 359 0 0 16 29.888889 360 0 0 17 30 361 0 0 36 41