## htsjdk.samtools.metrics.StringHeader # picard.analysis.CollectWgsMetrics INPUT=/gscratch/scrubbed/strigg/analyses/20200613/CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=CTRL_16C_26psu_2_S21_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 00:41:02 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 0.279502 1.089427 0 0 0.216464 0 0 0.013592 0.357375 0.001026 0.588456 0.159936 0.009565 0.001562 0.000321 0.000094 0.000045 0.000029 0.00002 0.000015 0.000013 0.000011 0.000009 0.000008 0.000007 0.113911 1 ## HISTOGRAM java.lang.Integer coverage high_quality_coverage_count 0 1749407641 1 233238442 2 50502032 3 19078887 4 10322200 5 6397486 6 4186468 7 2817929 8 1937911 9 1327073 10 929536 11 646671 12 455721 13 324207 14 227687 15 163612 16 117005 17 84827 18 62319 19 45211 20 33264 21 25088 22 19213 23 13943 24 11434 25 9241 26 7769 27 5656 28 4705 29 4342 30 3527 31 2680 32 2313 33 1999 34 2165 35 1792 36 1667 37 1242 38 1400 39 1221 40 1113 41 1208 42 965 43 1002 44 1052 45 1289 46 825 47 748 48 782 49 619 50 580 51 452 52 539 53 638 54 518 55 529 56 486 57 580 58 635 59 503 60 389 61 321 62 395 63 351 64 367 65 363 66 443 67 380 68 316 69 316 70 296 71 260 72 312 73 291 74 267 75 234 76 255 77 294 78 297 79 257 80 276 81 264 82 211 83 198 84 197 85 206 86 203 87 222 88 327 89 222 90 323 91 306 92 197 93 167 94 207 95 173 96 157 97 190 98 169 99 197 100 190 101 206 102 163 103 173 104 165 105 150 106 153 107 161 108 125 109 154 110 156 111 178 112 167 113 167 114 167 115 145 116 140 117 196 118 154 119 124 120 129 121 131 122 131 123 110 124 114 125 119 126 135 127 94 128 102 129 110 130 104 131 94 132 150 133 165 134 137 135 119 136 133 137 117 138 109 139 100 140 145 141 103 142 81 143 96 144 65 145 80 146 78 147 99 148 92 149 93 150 87 151 77 152 82 153 69 154 65 155 81 156 93 157 89 158 82 159 65 160 94 161 91 162 111 163 104 164 76 165 69 166 58 167 65 168 52 169 48 170 56 171 57 172 64 173 65 174 55 175 44 176 50 177 37 178 39 179 53 180 45 181 47 182 42 183 52 184 41 185 73 186 45 187 41 188 48 189 54 190 42 191 49 192 76 193 43 194 65 195 51 196 56 197 67 198 57 199 53 200 50 201 55 202 46 203 48 204 38 205 35 206 34 207 30 208 30 209 33 210 28 211 39 212 22 213 22 214 27 215 14 216 18 217 13 218 19 219 30 220 25 221 9 222 13 223 15 224 18 225 29 226 27 227 20 228 21 229 19 230 24 231 24 232 17 233 23 234 24 235 20 236 24 237 22 238 24 239 14 240 21 241 30 242 26 243 24 244 21 245 23 246 21 247 16 248 30 249 19 250 4323