## htsjdk.samtools.metrics.StringHeader # picard.analysis.CollectWgsMetrics INPUT=/gscratch/scrubbed/strigg/analyses/20200613/16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=16C_26psu_1_S13_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: Tue Jun 16 22:43:03 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 0.585809 1.480648 0 0 0.20618 0 0 0.015417 0.329953 0.000679 0.552229 0.327036 0.017242 0.003322 0.000816 0.000251 0.000106 0.000061 0.000035 0.000026 0.000021 0.000017 0.000015 0.000013 0.000012 0.219399 1 ## HISTOGRAM java.lang.Integer coverage high_quality_coverage_count 0 1401425663 1 438019029 2 138706539 3 47860205 4 20551614 5 11190145 6 7091681 7 4838992 8 3418741 9 2447338 10 1771490 11 1287944 12 942283 13 698476 14 518334 15 389287 16 286996 17 217452 18 162508 19 122234 20 93824 21 73660 22 55060 23 42610 24 35073 25 27876 26 21935 27 17877 28 14861 29 11961 30 10140 31 8243 32 6468 33 6292 34 5358 35 4780 36 4144 37 3565 38 3385 39 2753 40 2604 41 2322 42 2117 43 2109 44 2070 45 1632 46 1538 47 1495 48 1446 49 1186 50 1230 51 1197 52 996 53 1086 54 990 55 978 56 1099 57 851 58 900 59 755 60 713 61 831 62 753 63 692 64 681 65 680 66 700 67 679 68 498 69 664 70 530 71 529 72 467 73 488 74 478 75 425 76 396 77 531 78 476 79 463 80 435 81 438 82 350 83 337 84 396 85 407 86 347 87 337 88 271 89 266 90 411 91 353 92 308 93 270 94 255 95 213 96 228 97 253 98 251 99 261 100 223 101 216 102 214 103 223 104 275 105 215 106 196 107 213 108 236 109 273 110 250 111 281 112 236 113 246 114 194 115 250 116 225 117 239 118 230 119 243 120 208 121 187 122 180 123 221 124 239 125 228 126 241 127 240 128 204 129 162 130 224 131 208 132 167 133 230 134 204 135 192 136 181 137 185 138 172 139 178 140 155 141 155 142 104 143 127 144 127 145 138 146 140 147 107 148 134 149 147 150 168 151 147 152 158 153 163 154 165 155 156 156 151 157 129 158 129 159 113 160 120 161 143 162 131 163 122 164 116 165 114 166 116 167 113 168 112 169 107 170 103 171 100 172 75 173 109 174 118 175 122 176 115 177 98 178 110 179 106 180 93 181 109 182 88 183 93 184 100 185 94 186 96 187 99 188 124 189 100 190 58 191 64 192 62 193 66 194 79 195 73 196 71 197 73 198 72 199 52 200 70 201 62 202 58 203 77 204 55 205 62 206 44 207 53 208 63 209 44 210 59 211 50 212 55 213 39 214 53 215 52 216 46 217 35 218 47 219 54 220 47 221 45 222 48 223 54 224 46 225 51 226 47 227 63 228 56 229 38 230 52 231 44 232 37 233 37 234 45 235 34 236 41 237 29 238 26 239 47 240 48 241 41 242 54 243 39 244 28 245 37 246 35 247 32 248 33 249 29 250 7419