## htsjdk.samtools.metrics.StringHeader # CollectQualityYieldMetricsSNVQ INCLUDE_BQ_HISTOGRAM=true INPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5393-Z0079-CGCGCGCAGAATGAT/441525-L5393-Z0079-CGCGCGCAGAATGAT_sample.recal.bam OUTPUT=/Ddata/Runs/441525/output/441525-20260312_0210/441525-L5393-Z0079-CGCGCGCAGAATGAT/441525-L5393-Z0079-CGCGCGCAGAATGAT_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 02:54:24 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 999446 999446 116 116481103 116481103 111921932 111921932 103137879 103137879 0 0 0.960859 0.885447 0 0.960859 0.885447 0 349443309 349443309 343306778 343306778 329506710 329506710 306741941 306741941 0.982439 0.942948 0.877802 0.982439 0.942948 0.877802 ## HISTOGRAM java.lang.Integer KEY BQ_COUNT SNVQ_COUNT READ_INDEX_MEAN_BQ READ_INDEX_MEAN_SNVQ 0 812 0 35.992785 40.994608 1 9667 0 35.98631 40.99046 2 12149 3596 35.993718 40.994693 3 30789 1028 35.980192 40.983732 4 52694 41111 35.992281 40.9937 5 100685 15526 35.99591 40.996672 6 115802 109510 35.977762 40.980792 7 176293 144838 35.978423 40.984903 8 202730 148609 35.990051 40.9918 9 217290 98507 35.969419 40.974609 10 234123 505231 35.873359 40.928004 11 272811 54776 35.905692 40.928451 12 327531 673682 35.195973 40.318327 13 329023 197345 33.571481 39.494155 14 432241 944174 35.880949 40.926819 15 347657 339762 35.838817 40.888323 16 362788 459568 35.839363 40.859245 17 485906 1057525 35.905778 40.920217 18 504338 668623 35.67883 40.728556 19 343842 673120 35.606902 40.689624 20 463364 956571 35.856182 40.903239 21 609781 1234761 35.793597 40.849307 22 294875 522945 35.522705 40.67595 23 978781 1130925 35.134034 40.390575 24 526514 1018559 35.160888 40.423815 25 542768 426646 35.235579 40.482027 26 1697402 2448549 35.142616 40.405202 27 313636 760377 35.172716 40.434607 28 944083 337543 35.191976 40.449865 29 2412849 4963192 35.187732 40.444983 30 688823 38513 35.220722 40.466549 31 2179450 688475 35.214271 40.459153 32 1473749 5301164 35.196437 40.441798 33 759696 118200 35.216032 40.459308 34 2261518 2363083 35.2104 40.457882 35 1985759 3615790 35.230047 40.47196 36 93788884 1872821 35.257983 40.491908 37 0 3936139 35.265884 40.498371 38 0 312274 35.25752 40.493931 39 0 4518310 35.25235 40.488454 40 0 2 35.246099 40.484512 41 0 306741939 35.229774 40.471261 42 0 0 35.225642 40.468766 43 0 0 35.235227 40.47428 44 0 0 35.244702 40.481923 45 0 0 35.24887 40.48453 46 0 0 35.227601 40.469868 47 0 0 35.212286 40.457511 48 0 0 35.187243 40.439957 49 0 0 35.188999 40.441201 50 0 0 35.194803 40.446506 51 0 0 35.179627 40.434739 52 0 0 35.1358 40.403608 53 0 0 35.107322 40.393722 54 0 0 35.102486 40.388335 55 0 0 35.077224 40.369694 56 0 0 35.019638 40.338899 57 0 0 35.039975 40.339908 58 0 0 34.999428 40.308163 59 0 0 34.950366 40.270861 60 0 0 34.891375 40.226331 61 0 0 34.818629 40.172473 62 0 0 34.733281 40.107374 63 0 0 34.640096 40.037449 64 0 0 34.555186 39.971797 65 0 0 34.441555 39.888988 66 0 0 34.336829 39.810046 67 0 0 34.217941 39.722001 68 0 0 34.08828 39.625521 69 0 0 33.95698 39.523543 70 0 0 33.805475 39.403444 71 0 0 33.656967 39.283087 72 0 0 33.506882 39.16061 73 0 0 33.363243 39.043839 74 0 0 33.22475 38.93679 75 0 0 33.098796 38.835732 76 0 0 32.973722 38.741183 77 0 0 32.880295 38.666177 78 0 0 32.778265 38.586712 79 0 0 32.675121 38.507338 80 0 0 32.602736 38.444699 81 0 0 32.528974 38.384375 82 0 0 32.475165 38.335103 83 0 0 32.421637 38.289919 84 0 0 32.379866 38.255001 85 0 0 32.338073 38.218782 86 0 0 32.294111 38.177267 87 0 0 32.247516 38.138428 88 0 0 32.199149 38.093674 89 0 0 32.153543 38.057032 90 0 0 32.119522 38.026102 91 0 0 32.079965 37.987098 92 0 0 32.068277 37.972956 93 0 0 32.035746 37.943947 94 0 0 32.013605 37.924993 95 0 0 32.012242 37.92189 96 0 0 32.020463 37.927908 97 0 0 32.02266 37.926456 98 0 0 32.035373 37.937702 99 0 0 32.08161 37.978391 100 0 0 32.145714 38.025072 101 0 0 32.190903 38.059934 102 0 0 32.225643 38.089949 103 0 0 32.274924 38.124299 104 0 0 32.298196 38.141038 105 0 0 32.305969 38.143077 106 0 0 32.288792 38.125341 107 0 0 32.243828 38.088245 108 0 0 32.229568 38.073683 109 0 0 32.171977 38.034348 110 0 0 32.104756 37.977932 111 0 0 32.056027 37.941427 112 0 0 31.992472 37.888049 113 0 0 31.918381 37.828017 114 0 0 31.827925 37.758865 115 0 0 31.79097 37.733389 116 0 0 31.766928 37.715154 117 0 0 31.720727 37.67667 118 0 0 31.740275 37.695305 119 0 0 31.764075 37.711994 120 0 0 31.776469 37.720397 121 0 0 31.762364 37.705808 122 0 0 31.786876 37.727001 123 0 0 31.810905 37.741062 124 0 0 31.870989 37.786001 125 0 0 31.888401 37.794279 126 0 0 31.88413 37.791814 127 0 0 31.888784 37.786021 128 0 0 31.889982 37.781282 129 0 0 31.828071 37.721717 130 0 0 31.800491 37.697793 131 0 0 31.763319 37.668789 132 0 0 31.768681 37.673073 133 0 0 31.78921 37.688635 134 0 0 31.776626 37.684797 135 0 0 31.773787 37.677944 136 0 0 31.783004 37.690591 137 0 0 31.773957 37.680541 138 0 0 31.786781 37.694523 139 0 0 31.826314 37.723066 140 0 0 31.868379 37.760417 141 0 0 31.885504 37.767943 142 0 0 31.915168 37.796575 143 0 0 31.925705 37.799012 144 0 0 31.966953 37.833509 145 0 0 31.974065 37.832269 146 0 0 31.933239 37.795826 147 0 0 31.914446 37.7909 148 0 0 31.896878 37.772776 149 0 0 31.868012 37.748453 150 0 0 31.830939 37.709057 151 0 0 31.82918 37.711639 152 0 0 31.820478 37.701934 153 0 0 31.781443 37.680799 154 0 0 31.796738 37.690331 155 0 0 31.816105 37.706794 156 0 0 31.868399 37.7511 157 0 0 31.941025 37.814429 158 0 0 31.999685 37.849651 159 0 0 32.074774 37.906145 160 0 0 32.112392 37.943877 161 0 0 32.149732 37.969343 162 0 0 32.218072 38.020741 163 0 0 32.261732 38.061625 164 0 0 32.331061 38.113696 165 0 0 32.367814 38.139435 166 0 0 32.358677 38.13802 167 0 0 32.375616 38.144818 168 0 0 32.352623 38.127695 169 0 0 32.328518 38.102272 170 0 0 32.376356 38.148179 171 0 0 32.387322 38.146622 172 0 0 32.377787 38.151124 173 0 0 32.42473 38.188262 174 0 0 32.400087 38.174841 175 0 0 32.415551 38.202075 176 0 0 32.425931 38.206757 177 0 0 32.512344 38.279018 178 0 0 32.553553 38.302922 179 0 0 32.616155 38.354998 180 0 0 32.620545 38.364337 181 0 0 32.670755 38.411154 182 0 0 32.705309 38.441104 183 0 0 32.78147 38.506913 184 0 0 32.8775 38.578333 185 0 0 32.897985 38.597521 186 0 0 32.871013 38.586043 187 0 0 32.886077 38.594916 188 0 0 32.91476 38.615004 189 0 0 32.949434 38.632492 190 0 0 32.966991 38.651604 191 0 0 33.011477 38.688116 192 0 0 32.940886 38.649217 193 0 0 32.978551 38.674469 194 0 0 32.938849 38.652047 195 0 0 32.876813 38.611806 196 0 0 32.915852 38.64814 197 0 0 32.978984 38.693662 198 0 0 32.87311 38.6245 199 0 0 32.920128 38.678064 200 0 0 32.95235 38.694228 201 0 0 33.025777 38.762714 202 0 0 32.977978 38.726388 203 0 0 32.955432 38.704506 204 0 0 32.929959 38.684825 205 0 0 32.958627 38.716581 206 0 0 32.844905 38.655417 207 0 0 32.887228 38.678353 208 0 0 32.753264 38.582802 209 0 0 32.780587 38.614117 210 0 0 32.695985 38.552554 211 0 0 32.671621 38.534866 212 0 0 32.717164 38.589988 213 0 0 32.708757 38.582185 214 0 0 32.740142 38.607793 215 0 0 32.686336 38.546301 216 0 0 32.591092 38.498965 217 0 0 32.615945 38.531968 218 0 0 32.723792 38.595184 219 0 0 32.665916 38.539012 220 0 0 32.588446 38.504572 221 0 0 32.420046 38.371817 222 0 0 32.597128 38.502859 223 0 0 32.45824 38.431507 224 0 0 32.458486 38.431403 225 0 0 32.45319 38.41399 226 0 0 32.466501 38.421559 227 0 0 32.28324 38.319753 228 0 0 32.301423 38.296091 229 0 0 32.305934 38.338787 230 0 0 32.409705 38.369469 231 0 0 32.22961 38.273385 232 0 0 32.112252 38.197547 233 0 0 32.115504 38.191424 234 0 0 32.36154 38.361285 235 0 0 32.125256 38.207393 236 0 0 31.987441 38.056326 237 0 0 32.105263 38.176279 238 0 0 32.055556 38.219626 239 0 0 31.989676 38.112792 240 0 0 31.757626 37.972865 241 0 0 32.086272 38.186386 242 0 0 31.948323 38.141121 243 0 0 31.852419 38.050202 244 0 0 31.641392 37.934673 245 0 0 31.612636 37.881089 246 0 0 31.79654 38.010147 247 0 0 31.579707 37.854491 248 0 0 31.325522 37.648028 249 0 0 31.364177 37.697431 250 0 0 31.622517 37.911127 251 0 0 31.518761 37.802485 252 0 0 31.244951 37.646815 253 0 0 31.370568 37.714832 254 0 0 31.320099 37.746075 255 0 0 31.054779 37.546581 256 0 0 31.338 37.708095 257 0 0 31.153148 37.610444 258 0 0 31.024676 37.501053 259 0 0 31.048074 37.493991 260 0 0 30.859528 37.362625 261 0 0 31.184849 37.585626 262 0 0 30.681227 37.264977 263 0 0 30.645812 37.280114 264 0 0 30.618495 37.276489 265 0 0 30.435861 37.093903 266 0 0 30.480543 37.16838 267 0 0 30.562453 37.210434 268 0 0 30.361996 37.043634 269 0 0 30.561369 37.226987 270 0 0 29.974678 36.814443 271 0 0 30.181219 37.018259 272 0 0 29.965923 36.779835 273 0 0 30.099057 36.897799 274 0 0 29.762155 36.65192 275 0 0 29.905296 36.796529 276 0 0 29.538994 36.568836 277 0 0 29.514218 36.45545 278 0 0 29.772214 36.643594 279 0 0 29.539594 36.486802 280 0 0 29.338769 36.352446 281 0 0 29.60483 36.573363 282 0 0 29.622426 36.568459 283 0 0 29.221021 36.248048 284 0 0 29.211623 36.199832 285 0 0 29.472498 36.494588 286 0 0 28.95686 36.147336 287 0 0 29.034612 36.132681 288 0 0 29.179967 36.202769 289 0 0 28.867428 35.971027 290 0 0 29.382879 36.442458 291 0 0 28.574257 35.971617 292 0 0 28.978814 36.149011 293 0 0 28.903519 36.139614 294 0 0 28.971292 36.177831 295 0 0 28.894073 36.1467 296 0 0 29.158108 36.302703 297 0 0 29.007225 36.110308 298 0 0 28.758462 36.008718 299 0 0 27.97549 35.37963 300 0 0 28.449301 35.536713 301 0 0 28.516791 35.827114 302 0 0 28.627767 35.900067 303 0 0 29.387712 36.422316 304 0 0 28.307692 35.631222 305 0 0 27.982927 35.597561 306 0 0 28.710183 35.928634 307 0 0 28.505587 35.632216 308 0 0 28.39039 35.866867 309 0 0 28.496815 35.848195 310 0 0 28.043046 35.458057 311 0 0 28.007273 35.529697 312 0 0 28.854251 35.919028 313 0 0 28.534783 35.814493 314 0 0 28.042453 35.449686 315 0 0 27.934343 35.262626 316 0 0 27.544974 35.038801 317 0 0 26.988571 34.891429 318 0 0 28.614907 35.712215 319 0 0 27.798658 35.369128 320 0 0 27.792593 35.375309 321 0 0 27.907563 35.156863 322 0 0 27.657658 34.840841 323 0 0 27.893204 34.967638 324 0 0 27.817204 35.37276 325 0 0 27.270588 34.772549 326 0 0 27.381579 35.100877 327 0 0 27.076923 35.405128 328 0 0 26.685185 34.216049 329 0 0 25.588235 33.888889 330 0 0 27.021739 34.326087 331 0 0 26.3 34.308333 332 0 0 27.875 35.708333 333 0 0 28.076923 34.820513 334 0 0 29.222222 36 335 0 0 28.666667 36.111111 336 0 0 28.642857 35.666667 337 0 0 28.076923 35.307692 338 0 0 28.363636 36.151515 339 0 0 29 35.555556 340 0 0 31.222222 38.074074 341 0 0 22.375 31.541667 342 0 0 26.285714 34.857143 343 0 0 19.8 30 344 0 0 27.8 35.666667 345 0 0 33.333333 38 346 0 0 20.5 34.333333 347 0 0 16 27.333333 348 0 0 10.5 21.333333 349 0 0 16.5 26.666667