## htsjdk.samtools.metrics.StringHeader # picard.analysis.CollectWgsMetrics INPUT=/gscratch/scrubbed/strigg/analyses/20200613/16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=16C_32psu_4_S4_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 23:32:55 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 0.457753 1.053343 0 0 0.202757 0 0 0.016335 0.301549 0.000421 0.521062 0.303653 0.006358 0.000533 0.00011 0.00005 0.000033 0.000026 0.000019 0.000015 0.000013 0.000011 0.000009 0.000008 0.000007 0.194034 1 ## HISTOGRAM java.lang.Integer coverage high_quality_coverage_count 0 1450119867 1 439751801 2 127897283 3 38020844 4 13438093 5 5893509 6 3021772 7 1662375 8 981668 9 571691 10 356499 11 224372 12 141609 13 94205 14 64211 15 41900 16 31546 17 21412 18 16745 19 13091 20 10825 21 7775 22 6295 23 5632 24 4164 25 3788 26 3166 27 3116 28 2739 29 2511 30 2557 31 1981 32 1861 33 1637 34 1450 35 1404 36 1157 37 1399 38 1118 39 988 40 987 41 1057 42 810 43 788 44 858 45 868 46 647 47 629 48 592 49 439 50 495 51 443 52 450 53 501 54 538 55 539 56 483 57 501 58 436 59 445 60 424 61 342 62 436 63 393 64 374 65 370 66 300 67 306 68 280 69 323 70 307 71 354 72 326 73 278 74 252 75 256 76 276 77 251 78 243 79 330 80 225 81 242 82 249 83 227 84 228 85 213 86 207 87 232 88 274 89 249 90 209 91 225 92 245 93 265 94 253 95 233 96 222 97 254 98 217 99 204 100 227 101 189 102 167 103 188 104 188 105 182 106 211 107 222 108 229 109 219 110 166 111 145 112 132 113 133 114 165 115 191 116 205 117 170 118 138 119 174 120 160 121 166 122 151 123 156 124 179 125 133 126 125 127 148 128 121 129 97 130 104 131 82 132 117 133 119 134 104 135 95 136 97 137 78 138 92 139 58 140 69 141 78 142 94 143 108 144 100 145 88 146 81 147 65 148 80 149 77 150 94 151 76 152 69 153 85 154 74 155 78 156 72 157 90 158 74 159 63 160 76 161 93 162 67 163 70 164 87 165 57 166 44 167 34 168 41 169 32 170 32 171 48 172 43 173 39 174 52 175 50 176 37 177 44 178 41 179 52 180 30 181 32 182 45 183 44 184 49 185 48 186 33 187 44 188 45 189 51 190 45 191 34 192 31 193 41 194 33 195 44 196 50 197 47 198 34 199 38 200 26 201 42 202 27 203 28 204 54 205 42 206 44 207 32 208 34 209 33 210 43 211 24 212 44 213 49 214 46 215 33 216 26 217 40 218 35 219 69 220 37 221 37 222 43 223 39 224 34 225 31 226 26 227 24 228 25 229 23 230 29 231 17 232 22 233 28 234 20 235 24 236 23 237 13 238 13 239 17 240 21 241 21 242 30 243 17 244 20 245 23 246 13 247 26 248 30 249 33 250 4015