## htsjdk.samtools.metrics.StringHeader # picard.analysis.CollectWgsMetrics INPUT=/gscratch/scrubbed/strigg/analyses/20200516/Mcap_tg/nodedup/Mcap_RRBS_100M_R1_001_val_1_bismark_bt2_pe.sorted.bam OUTPUT=Mcap_RRBS_100M_R1_001_val_1_bismark_bt2_pe.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 10:59:44 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 5.691618 28.688225 0 0 0.297153 0 0 0.008837 0.24466 0.039772 0.590421 0.114897 0.072616 0.06488 0.05884 0.053767 0.049384 0.04563 0.039499 0.034782 0.030966 0.027787 0.025115 0.022738 0.020651 0.098094 0 ## HISTOGRAM java.lang.Integer coverage high_quality_coverage_count 0 783940043 1 24203454 2 7767278 3 3387177 4 2090600 5 1622248 6 1434612 7 1339705 8 1242629 9 1212118 10 1165936 11 1102170 12 1059738 13 1028363 14 993756 15 943243 16 935565 17 899126 18 864843 19 850466 20 823846 21 792671 22 779541 23 757382 24 728551 25 697772 26 681869 27 663600 28 657783 29 624100 30 603599 31 596531 32 586175 33 567831 34 553970 35 532084 36 525280 37 495285 38 492814 39 476205 40 449838 41 451901 42 441584 43 433531 44 416749 45 411214 46 404179 47 395709 48 391877 49 381657 50 364756 51 363262 52 370434 53 353059 54 336801 55 330162 56 320143 57 311747 58 314570 59 314910 60 308659 61 296259 62 286125 63 288263 64 281226 65 277611 66 274293 67 273395 68 266809 69 262716 70 264722 71 248805 72 235159 73 234284 74 228455 75 232212 76 232484 77 229567 78 229695 79 231050 80 229484 81 227134 82 217702 83 213646 84 214443 85 204854 86 204999 87 201720 88 197515 89 193662 90 194645 91 195525 92 191587 93 188086 94 181534 95 178343 96 184509 97 185092 98 173417 99 176494 100 168296 101 164790 102 160916 103 158713 104 154947 105 154489 106 154844 107 150106 108 149117 109 156484 110 147471 111 145697 112 146380 113 141794 114 144369 115 142080 116 137211 117 140559 118 140666 119 137358 120 138556 121 138096 122 134348 123 124402 124 127312 125 123870 126 127855 127 123389 128 123972 129 129479 130 121198 131 120205 132 121206 133 122236 134 117177 135 113388 136 116225 137 112985 138 113734 139 108157 140 106722 141 106974 142 110434 143 107686 144 106312 145 101616 146 101368 147 101637 148 95868 149 95938 150 97886 151 96367 152 96301 153 95262 154 94224 155 93567 156 95905 157 93055 158 91949 159 91246 160 91239 161 90149 162 86875 163 86037 164 89749 165 88412 166 86131 167 85627 168 83875 169 82762 170 82960 171 84129 172 83374 173 78925 174 78725 175 82008 176 77278 177 78535 178 80475 179 74264 180 77391 181 77721 182 75205 183 71615 184 72649 185 75166 186 74095 187 74013 188 72249 189 73600 190 70680 191 70206 192 69387 193 70952 194 70287 195 67222 196 66169 197 66711 198 67384 199 67356 200 65247 201 66030 202 62484 203 65144 204 63239 205 67075 206 62715 207 63523 208 63548 209 62640 210 58880 211 62974 212 61757 213 58446 214 58001 215 56927 216 58662 217 56397 218 59995 219 55704 220 56563 221 60157 222 57368 223 55495 224 55606 225 54709 226 52593 227 55368 228 56151 229 55139 230 55999 231 53548 232 54298 233 55013 234 51409 235 50216 236 52756 237 51031 238 47244 239 50347 240 48795 241 47077 242 51992 243 51467 244 46679 245 47634 246 48200 247 46638 248 47177 249 45891 250 4962347