## htsjdk.samtools.metrics.StringHeader # picard.analysis.CollectWgsMetrics INPUT=/gscratch/scrubbed/strigg/analyses/20200613/8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=8C_32psu_4_S8_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 00:27:17 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 0.393371 1.168285 0 0 0.211341 0 0 0.015427 0.319302 0.000633 0.546702 0.240413 0.01027 0.001588 0.000349 0.000113 0.000053 0.000034 0.000022 0.000017 0.000014 0.000012 0.00001 0.000009 0.000008 0.158218 1 ## HISTOGRAM java.lang.Integer coverage high_quality_coverage_count 0 1581815249 1 351422073 2 87260140 3 27918047 4 12665918 5 7216477 6 4550759 7 2980363 8 1997229 9 1336130 10 930085 11 639262 12 456017 13 322112 14 232571 15 166865 16 123069 17 88840 18 64539 19 48435 20 39351 21 31198 22 23074 23 17397 24 13567 25 11278 26 8789 27 7383 28 6016 29 5297 30 4482 31 3799 32 3164 33 2605 34 2738 35 2404 36 2007 37 1851 38 1653 39 1593 40 1578 41 1306 42 1383 43 984 44 911 45 961 46 850 47 679 48 720 49 678 50 627 51 694 52 609 53 573 54 611 55 621 56 542 57 482 58 432 59 451 60 480 61 574 62 498 63 470 64 430 65 428 66 383 67 384 68 410 69 400 70 472 71 426 72 386 73 427 74 424 75 318 76 322 77 295 78 332 79 273 80 283 81 373 82 263 83 296 84 281 85 238 86 264 87 310 88 247 89 281 90 254 91 257 92 197 93 175 94 169 95 228 96 271 97 202 98 274 99 203 100 245 101 177 102 195 103 189 104 232 105 165 106 163 107 152 108 137 109 185 110 196 111 159 112 131 113 119 114 150 115 152 116 135 117 144 118 159 119 197 120 157 121 139 122 101 123 98 124 114 125 129 126 173 127 119 128 106 129 75 130 93 131 94 132 91 133 84 134 91 135 68 136 86 137 71 138 88 139 80 140 103 141 90 142 90 143 74 144 60 145 77 146 120 147 64 148 74 149 65 150 72 151 61 152 95 153 71 154 91 155 52 156 55 157 71 158 35 159 61 160 63 161 64 162 46 163 70 164 62 165 50 166 62 167 42 168 56 169 57 170 75 171 49 172 62 173 82 174 61 175 59 176 60 177 49 178 44 179 46 180 54 181 64 182 63 183 69 184 65 185 63 186 59 187 40 188 62 189 70 190 57 191 45 192 54 193 42 194 41 195 45 196 33 197 45 198 44 199 41 200 43 201 41 202 49 203 45 204 38 205 63 206 50 207 37 208 32 209 45 210 43 211 32 212 26 213 30 214 45 215 32 216 28 217 33 218 29 219 27 220 21 221 19 222 27 223 23 224 29 225 21 226 32 227 32 228 24 229 30 230 20 231 23 232 23 233 27 234 30 235 29 236 33 237 30 238 32 239 36 240 44 241 33 242 33 243 36 244 28 245 21 246 21 247 29 248 25 249 32 250 5234