## htsjdk.samtools.metrics.StringHeader # picard.analysis.CollectWgsMetrics INPUT=/gscratch/scrubbed/strigg/analyses/20200613/8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=8C_32psu_1_S5_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 00:07:35 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 0.302323 1.130265 0 0 0.189141 0 0 0.01389 0.372775 0.000858 0.576663 0.173565 0.010172 0.001684 0.000363 0.000112 0.000053 0.000034 0.000022 0.000017 0.000014 0.000012 0.00001 0.000009 0.000008 0.124002 1 ## HISTOGRAM java.lang.Integer coverage high_quality_coverage_count 0 1721024488 1 252883457 2 55898874 3 20547539 4 10931634 5 6776871 6 4469706 7 2983767 8 2035013 9 1410449 10 981563 11 690616 12 481609 13 345351 14 251426 15 181115 16 127569 17 93755 18 69318 19 51378 20 37723 21 29751 22 23769 23 17931 24 14014 25 11430 26 9072 27 7056 28 5869 29 4840 30 4236 31 3613 32 3183 33 2760 34 2729 35 2265 36 2011 37 2016 38 1874 39 1659 40 1361 41 1556 42 1168 43 1030 44 912 45 831 46 990 47 852 48 939 49 834 50 770 51 671 52 770 53 593 54 664 55 593 56 651 57 533 58 512 59 469 60 455 61 514 62 443 63 352 64 324 65 439 66 361 67 388 68 543 69 420 70 405 71 387 72 347 73 341 74 333 75 358 76 399 77 352 78 312 79 264 80 291 81 259 82 231 83 273 84 300 85 311 86 225 87 249 88 243 89 265 90 230 91 207 92 189 93 212 94 223 95 208 96 251 97 260 98 227 99 219 100 178 101 194 102 215 103 206 104 183 105 240 106 173 107 192 108 162 109 157 110 189 111 191 112 159 113 152 114 159 115 200 116 172 117 147 118 139 119 118 120 149 121 133 122 143 123 127 124 107 125 113 126 112 127 122 128 115 129 114 130 131 131 112 132 113 133 134 134 98 135 99 136 98 137 133 138 174 139 104 140 87 141 92 142 100 143 86 144 81 145 90 146 85 147 63 148 73 149 82 150 79 151 84 152 85 153 84 154 83 155 87 156 74 157 101 158 76 159 76 160 73 161 55 162 66 163 59 164 69 165 64 166 79 167 45 168 56 169 63 170 79 171 61 172 74 173 58 174 61 175 68 176 42 177 64 178 44 179 59 180 58 181 46 182 44 183 40 184 37 185 42 186 33 187 38 188 34 189 46 190 49 191 65 192 73 193 51 194 33 195 37 196 53 197 32 198 35 199 37 200 28 201 31 202 29 203 31 204 46 205 40 206 37 207 36 208 28 209 41 210 34 211 44 212 28 213 41 214 34 215 44 216 44 217 35 218 38 219 31 220 28 221 32 222 36 223 30 224 28 225 47 226 26 227 27 228 28 229 20 230 33 231 33 232 17 233 16 234 22 235 21 236 21 237 14 238 14 239 7 240 18 241 28 242 19 243 29 244 35 245 23 246 21 247 18 248 30 249 26 250 4874