## htsjdk.samtools.metrics.StringHeader # picard.analysis.CollectWgsMetrics INPUT=/gscratch/scrubbed/strigg/analyses/20200613/CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=CTRL_8C_26psu_2_S18_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 00:54:13 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 0.333117 1.184368 0 0 0.19666 0 0 0.014257 0.367915 0.00057 0.579403 0.190067 0.011051 0.00212 0.000546 0.00019 0.000087 0.00005 0.000027 0.000018 0.000014 0.000011 0.000009 0.000008 0.000007 0.135282 1 ## HISTOGRAM java.lang.Integer coverage high_quality_coverage_count 0 1686659539 1 276327328 2 63033118 3 22124537 4 11309918 5 6975852 6 4645591 7 3182723 8 2221104 9 1574049 10 1122392 11 811123 12 592009 13 435694 14 317055 15 237630 16 178291 17 137364 18 105883 19 82008 20 64873 21 52233 22 40011 23 31691 24 25268 25 21734 26 17998 27 14542 28 12216 29 10222 30 8471 31 7125 32 5952 33 5298 34 4936 35 4447 36 3982 37 3090 38 3028 39 2868 40 2602 41 2145 42 2040 43 1752 44 1766 45 1664 46 1614 47 1312 48 1255 49 1277 50 1243 51 1143 52 1045 53 954 54 947 55 902 56 790 57 768 58 756 59 573 60 731 61 638 62 781 63 619 64 539 65 548 66 553 67 408 68 526 69 408 70 511 71 501 72 451 73 389 74 384 75 397 76 293 77 362 78 377 79 331 80 292 81 274 82 245 83 291 84 312 85 294 86 297 87 244 88 311 89 245 90 289 91 224 92 231 93 270 94 229 95 248 96 221 97 229 98 215 99 198 100 156 101 146 102 145 103 201 104 207 105 195 106 196 107 173 108 217 109 193 110 174 111 169 112 141 113 152 114 151 115 113 116 137 117 103 118 147 119 170 120 164 121 107 122 176 123 93 124 122 125 121 126 107 127 76 128 92 129 91 130 109 131 95 132 117 133 129 134 88 135 87 136 68 137 69 138 84 139 81 140 103 141 94 142 74 143 62 144 65 145 55 146 74 147 59 148 69 149 66 150 79 151 93 152 75 153 91 154 60 155 77 156 83 157 63 158 71 159 67 160 55 161 78 162 67 163 77 164 67 165 66 166 65 167 75 168 63 169 90 170 61 171 71 172 73 173 39 174 67 175 47 176 37 177 38 178 34 179 28 180 23 181 30 182 44 183 50 184 59 185 66 186 42 187 43 188 40 189 37 190 27 191 23 192 24 193 39 194 37 195 33 196 42 197 14 198 26 199 20 200 27 201 36 202 36 203 14 204 17 205 23 206 15 207 13 208 13 209 10 210 25 211 17 212 22 213 22 214 13 215 25 216 23 217 16 218 15 219 15 220 14 221 21 222 17 223 10 224 15 225 14 226 13 227 15 228 19 229 8 230 19 231 16 232 14 233 22 234 18 235 12 236 25 237 28 238 17 239 13 240 16 241 13 242 15 243 14 244 19 245 15 246 8 247 13 248 18 249 13 250 4419