## htsjdk.samtools.metrics.StringHeader # picard.analysis.CollectWgsMetrics INPUT=/gscratch/scrubbed/strigg/analyses/20200613/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt REFERENCE_SEQUENCE=/gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.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: Wed Jun 17 00:47:28 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 2082468696 0.386142 1.021418 0 0 0.19479 0 0 0.015173 0.312157 0.000334 0.522454 0.258147 0.005781 0.000783 0.00024 0.00011 0.000063 0.00004 0.000022 0.000015 0.000012 0.000009 0.000008 0.000007 0.000006 0.166318 1 ## HISTOGRAM java.lang.Integer coverage high_quality_coverage_count 0 1544885739 1 385782596 2 100254828 3 28970454 4 10536279 5 4837212 6 2545500 7 1494719 8 927775 9 603936 10 403577 11 278674 12 198711 13 142988 14 105467 15 81469 16 66125 17 50774 18 38944 19 32819 20 27174 21 23008 22 19605 23 15913 24 13920 25 12172 26 10722 27 9530 28 7850 29 7120 30 6240 31 5173 32 4771 33 4384 34 3360 35 3063 36 2856 37 2893 38 2619 39 2269 40 2034 41 2170 42 1718 43 1508 44 1496 45 1383 46 1175 47 1164 48 1117 49 1059 50 833 51 814 52 740 53 707 54 824 55 584 56 569 57 549 58 537 59 440 60 495 61 542 62 471 63 462 64 447 65 477 66 413 67 359 68 375 69 398 70 415 71 393 72 372 73 411 74 303 75 275 76 267 77 305 78 396 79 315 80 325 81 317 82 243 83 244 84 197 85 238 86 276 87 211 88 191 89 244 90 259 91 254 92 219 93 182 94 165 95 156 96 146 97 155 98 154 99 173 100 146 101 140 102 137 103 176 104 174 105 167 106 140 107 125 108 116 109 138 110 101 111 129 112 145 113 137 114 109 115 120 116 108 117 95 118 92 119 94 120 72 121 90 122 78 123 84 124 90 125 108 126 104 127 101 128 89 129 102 130 65 131 103 132 98 133 67 134 86 135 62 136 75 137 73 138 102 139 86 140 76 141 146 142 78 143 53 144 51 145 61 146 51 147 60 148 53 149 50 150 65 151 73 152 57 153 43 154 57 155 63 156 49 157 50 158 40 159 41 160 42 161 42 162 54 163 68 164 52 165 60 166 48 167 42 168 35 169 36 170 47 171 33 172 31 173 45 174 44 175 61 176 38 177 59 178 75 179 36 180 29 181 32 182 25 183 38 184 47 185 54 186 71 187 45 188 45 189 34 190 27 191 30 192 29 193 30 194 20 195 19 196 45 197 41 198 29 199 32 200 39 201 42 202 37 203 36 204 32 205 22 206 24 207 35 208 30 209 47 210 45 211 29 212 34 213 17 214 36 215 19 216 27 217 30 218 34 219 33 220 27 221 30 222 29 223 29 224 30 225 32 226 32 227 23 228 39 229 35 230 43 231 43 232 33 233 25 234 22 235 30 236 19 237 19 238 20 239 39 240 30 241 39 242 33 243 23 244 28 245 27 246 38 247 24 248 37 249 24 250 3046