## htsjdk.samtools.metrics.StringHeader # picard.analysis.CollectWgsMetrics INPUT=/gscratch/scrubbed/strigg/analyses/20200516/Mcap_tg/dedup/Mcap_MBD_100M_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=Mcap_MBD_100M_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 09:52:39 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 0.777845 1.453438 0 0 0.434349 0 0 0.008394 0.191959 0.00001 0.634713 0.373352 0.025333 0.000781 0.000173 0.000105 0.000078 0.000061 0.000041 0.000029 0.000021 0.000016 0.000013 0.000011 0.000009 0.249636 1 ## HISTOGRAM java.lang.Integer coverage high_quality_coverage_count 0 555024564 1 156324984 2 83310988 3 45095719 4 23510305 5 11721073 6 5616935 7 2625010 8 1214742 9 568809 10 268587 11 132499 12 70305 13 40146 14 26498 15 19015 16 14028 17 11305 18 8570 19 7294 20 5953 21 5183 22 5018 23 4226 24 3869 25 3576 26 3041 27 3164 28 2715 29 2565 30 2219 31 2023 32 1776 33 1774 34 1764 35 1855 36 1652 37 1536 38 1429 39 1424 40 1328 41 1317 42 1185 43 1036 44 1162 45 1140 46 1058 47 875 48 798 49 857 50 793 51 789 52 728 53 683 54 717 55 689 56 618 57 615 58 645 59 646 60 569 61 517 62 418 63 441 64 445 65 445 66 375 67 316 68 308 69 344 70 300 71 320 72 279 73 234 74 231 75 245 76 272 77 264 78 246 79 265 80 217 81 266 82 267 83 272 84 197 85 172 86 180 87 208 88 190 89 140 90 181 91 168 92 204 93 207 94 210 95 200 96 232 97 195 98 207 99 223 100 235 101 236 102 244 103 232 104 221 105 196 106 170 107 147 108 160 109 139 110 134 111 132 112 97 113 112 114 131 115 124 116 109 117 119 118 96 119 119 120 105 121 118 122 127 123 117 124 95 125 71 126 96 127 97 128 113 129 81 130 64 131 105 132 111 133 106 134 95 135 95 136 91 137 73 138 73 139 83 140 80 141 79 142 74 143 75 144 63 145 84 146 72 147 55 148 66 149 57 150 59 151 47 152 39 153 54 154 41 155 49 156 46 157 46 158 51 159 37 160 36 161 41 162 46 163 40 164 44 165 58 166 30 167 41 168 36 169 18 170 28 171 20 172 12 173 11 174 15 175 19 176 26 177 18 178 17 179 9 180 13 181 18 182 12 183 6 184 8 185 14 186 12 187 9 188 12 189 11 190 17 191 9 192 15 193 17 194 19 195 11 196 12 197 14 198 11 199 12 200 8 201 8 202 2 203 2 204 5 205 5 206 4 207 5 208 5 209 5 210 4 211 2 212 10 213 10 214 8 215 7 216 9 217 5 218 5 219 9 220 7 221 6 222 7 223 7 224 8 225 7 226 4 227 7 228 5 229 4 230 4 231 2 232 6 233 4 234 6 235 4 236 3 237 5 238 2 239 2 240 2 241 10 242 7 243 2 244 5 245 3 246 7 247 2 248 6 249 9 250 380