## htsjdk.samtools.metrics.StringHeader # picard.analysis.CollectWgsMetrics INPUT=/gscratch/scrubbed/strigg/analyses/20200613/16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=16C_26psu_4_S16_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 23:04:28 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 0.450309 1.175543 0 0 0.204977 0 0 0.015109 0.331058 0.000398 0.551542 0.278432 0.01022 0.00146 0.000341 0.000124 0.000063 0.000041 0.000024 0.000017 0.000014 0.000012 0.00001 0.000008 0.000007 0.185814 1 ## HISTOGRAM java.lang.Integer coverage high_quality_coverage_count 0 1502642854 1 399053613 2 110150597 3 34883144 4 14456426 5 7631497 6 4547617 7 2906091 8 1900459 9 1255024 10 853249 11 583415 12 403460 13 285256 14 205844 15 147857 16 111075 17 83168 18 62434 19 47541 20 37251 21 30084 22 24421 23 19224 24 16787 25 12799 26 10152 27 8746 28 7373 29 6679 30 5942 31 4978 32 4390 33 3797 34 3195 35 2858 36 2750 37 2213 38 2067 39 1887 40 1705 41 1837 42 1736 43 1458 44 1399 45 1429 46 1280 47 1254 48 1133 49 1091 50 1076 51 911 52 840 53 992 54 746 55 569 56 685 57 549 58 497 59 622 60 555 61 505 62 440 63 435 64 475 65 366 66 352 67 317 68 298 69 314 70 276 71 366 72 404 73 363 74 336 75 410 76 388 77 355 78 362 79 427 80 354 81 339 82 304 83 350 84 281 85 356 86 394 87 323 88 357 89 256 90 301 91 297 92 314 93 388 94 318 95 306 96 296 97 248 98 205 99 264 100 251 101 227 102 204 103 183 104 188 105 190 106 187 107 163 108 177 109 187 110 195 111 195 112 178 113 214 114 213 115 153 116 147 117 199 118 152 119 131 120 121 121 129 122 121 123 149 124 125 125 115 126 123 127 86 128 100 129 73 130 85 131 122 132 106 133 80 134 72 135 74 136 87 137 75 138 84 139 106 140 82 141 97 142 77 143 71 144 74 145 81 146 69 147 64 148 55 149 47 150 67 151 80 152 84 153 76 154 75 155 67 156 73 157 60 158 59 159 69 160 51 161 58 162 67 163 57 164 76 165 53 166 47 167 77 168 39 169 55 170 43 171 38 172 44 173 52 174 47 175 50 176 42 177 45 178 47 179 34 180 28 181 28 182 37 183 43 184 45 185 43 186 58 187 39 188 43 189 48 190 28 191 49 192 59 193 44 194 39 195 35 196 29 197 37 198 40 199 48 200 41 201 50 202 29 203 41 204 31 205 28 206 39 207 49 208 41 209 36 210 29 211 31 212 32 213 32 214 35 215 29 216 35 217 30 218 21 219 25 220 36 221 32 222 42 223 26 224 24 225 39 226 45 227 30 228 29 229 25 230 27 231 33 232 19 233 34 234 30 235 33 236 23 237 20 238 17 239 16 240 25 241 23 242 20 243 27 244 19 245 16 246 31 247 27 248 14 249 29 250 4147