## htsjdk.samtools.metrics.StringHeader # picard.analysis.CollectWgsMetrics INPUT=/gscratch/scrubbed/strigg/analyses/20200516/Mcap_tg/dedup/Mcap_WGBS_150M_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=Mcap_WGBS_150M_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt REFERENCE_SEQUENCE=/gscratch/srlab/sr320/data/froger/Mcap_Genome/Mcap.genome_assembly.fa MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json ## htsjdk.samtools.metrics.StringHeader # Started on: Thu May 28 10:25:56 PDT 2020 ## METRICS CLASS picard.analysis.CollectWgsMetrics$WgsMetrics GENOME_TERRITORY MEAN_COVERAGE SD_COVERAGE MEDIAN_COVERAGE MAD_COVERAGE PCT_EXC_MAPQ PCT_EXC_DUPE PCT_EXC_UNPAIRED PCT_EXC_BASEQ PCT_EXC_OVERLAP PCT_EXC_CAPPED PCT_EXC_TOTAL PCT_1X PCT_5X PCT_10X PCT_15X PCT_20X PCT_25X PCT_30X PCT_40X PCT_50X PCT_60X PCT_70X PCT_80X PCT_90X PCT_100X HET_SNP_SENSITIVITY HET_SNP_Q 885704498 3.507356 4.817834 1 1 0.408228 0 0 0.00839 0.181376 0.000176 0.59817 0.616385 0.300743 0.117523 0.033429 0.00742 0.001667 0.000549 0.000196 0.000129 0.000104 0.000089 0.000079 0.00007 0.000062 0.501739 3 ## HISTOGRAM java.lang.Integer coverage high_quality_coverage_count 0 339769376 1 104128177 2 71854327 3 56398806 4 47184723 5 40999361 6 36283273 7 32150224 8 28262656 9 24583019 10 20995852 11 17641542 12 14600608 13 11831117 14 9413358 15 7389521 16 5693254 17 4317978 18 3234732 19 2400494 20 1758219 21 1274003 22 923004 23 665432 24 474641 25 339280 26 245692 27 179391 28 131003 29 95525 30 71678 31 56393 32 43413 33 33970 34 27326 35 21711 36 18416 37 15425 38 12557 39 11072 40 9377 41 8751 42 7786 43 6692 44 5795 45 5053 46 4774 47 4185 48 3824 49 3691 50 3205 51 2886 52 2588 53 2415 54 2083 55 2059 56 1921 57 1874 58 1639 59 1551 60 1454 61 1393 62 1289 63 1453 64 1298 65 1231 66 1263 67 1123 68 1019 69 1139 70 1019 71 1065 72 952 73 987 74 962 75 900 76 901 77 859 78 862 79 808 80 815 81 775 82 819 83 810 84 742 85 810 86 726 87 760 88 761 89 686 90 721 91 762 92 797 93 769 94 798 95 715 96 652 97 654 98 607 99 606 100 557 101 532 102 568 103 567 104 556 105 527 106 561 107 511 108 513 109 532 110 541 111 602 112 592 113 546 114 523 115 490 116 458 117 498 118 475 119 526 120 542 121 520 122 516 123 534 124 440 125 457 126 419 127 460 128 407 129 422 130 384 131 392 132 391 133 377 134 399 135 405 136 403 137 341 138 387 139 359 140 375 141 343 142 395 143 343 144 403 145 341 146 390 147 443 148 382 149 325 150 342 151 317 152 302 153 310 154 299 155 300 156 259 157 287 158 274 159 250 160 266 161 238 162 280 163 243 164 250 165 286 166 272 167 263 168 297 169 250 170 250 171 252 172 258 173 243 174 238 175 269 176 243 177 212 178 256 179 235 180 205 181 237 182 202 183 188 184 192 185 216 186 210 187 219 188 222 189 234 190 208 191 238 192 217 193 218 194 229 195 208 196 197 197 183 198 195 199 184 200 144 201 174 202 191 203 178 204 190 205 170 206 178 207 183 208 183 209 147 210 170 211 141 212 141 213 151 214 153 215 141 216 181 217 188 218 189 219 170 220 159 221 152 222 152 223 157 224 150 225 147 226 148 227 139 228 127 229 151 230 170 231 113 232 119 233 102 234 103 235 106 236 104 237 131 238 98 239 145 240 132 241 140 242 139 243 134 244 119 245 127 246 132 247 134 248 128 249 108 250 12496