## htsjdk.samtools.metrics.StringHeader # picard.analysis.CollectWgsMetrics INPUT=/gscratch/scrubbed/strigg/analyses/20200516/Mcap_tg/dedup/Mcap_MBD_200M_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=Mcap_MBD_200M_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 10:04:40 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 0.962261 1.732367 0 0 0.446994 0 0 0.008269 0.188642 0.000021 0.643927 0.409926 0.043062 0.001913 0.000277 0.000145 0.000103 0.000081 0.000055 0.00004 0.00003 0.000023 0.000019 0.000016 0.000013 0.282112 1 ## HISTOGRAM java.lang.Integer coverage high_quality_coverage_count 0 522630762 1 152291201 2 88376395 3 53124762 4 31141036 5 17668075 6 9642510 7 5123145 8 2648597 9 1363924 10 704772 11 371849 12 196884 13 111299 14 64341 15 41551 16 27808 17 19891 18 15259 19 12063 20 9727 21 8236 22 6931 23 6194 24 5796 25 5021 26 4414 27 3992 28 3567 29 3166 30 2856 31 2750 32 2733 33 2837 34 2370 35 2167 36 1911 37 1725 38 1635 39 1534 40 1550 41 1382 42 1504 43 1453 44 1392 45 1360 46 1401 47 1203 48 1153 49 1107 50 996 51 1043 52 978 53 869 54 808 55 920 56 841 57 834 58 689 59 738 60 687 61 661 62 635 63 563 64 576 65 590 66 605 67 595 68 521 69 543 70 464 71 487 72 463 73 429 74 385 75 373 76 377 77 324 78 308 79 349 80 315 81 316 82 290 83 337 84 258 85 308 86 276 87 242 88 254 89 263 90 240 91 253 92 197 93 214 94 217 95 221 96 207 97 226 98 202 99 218 100 192 101 162 102 160 103 191 104 163 105 163 106 150 107 151 108 144 109 153 110 141 111 102 112 110 113 130 114 149 115 186 116 179 117 152 118 197 119 204 120 169 121 161 122 200 123 162 124 158 125 143 126 136 127 140 128 148 129 151 130 176 131 148 132 155 133 153 134 165 135 173 136 169 137 172 138 165 139 152 140 133 141 116 142 89 143 90 144 90 145 110 146 92 147 96 148 98 149 89 150 77 151 86 152 75 153 100 154 93 155 85 156 83 157 82 158 61 159 51 160 60 161 68 162 75 163 57 164 88 165 71 166 60 167 57 168 58 169 45 170 46 171 41 172 61 173 51 174 46 175 62 176 64 177 60 178 57 179 43 180 49 181 41 182 41 183 38 184 42 185 47 186 48 187 53 188 40 189 33 190 33 191 36 192 38 193 42 194 49 195 38 196 46 197 42 198 31 199 32 200 20 201 39 202 23 203 36 204 23 205 29 206 24 207 25 208 19 209 31 210 29 211 30 212 23 213 30 214 17 215 25 216 15 217 15 218 12 219 16 220 16 221 9 222 14 223 12 224 14 225 15 226 23 227 14 228 19 229 14 230 11 231 12 232 6 233 6 234 10 235 8 236 7 237 6 238 7 239 7 240 9 241 16 242 14 243 10 244 12 245 9 246 10 247 12 248 4 249 6 250 629