## htsjdk.samtools.metrics.StringHeader # picard.analysis.CollectWgsMetrics INPUT=/gscratch/scrubbed/strigg/analyses/20200613/16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=16C_26psu_2_S14_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 22:50:57 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 0.445899 1.193289 0 0 0.210746 0 0 0.015291 0.320917 0.000437 0.54739 0.272977 0.01087 0.001618 0.000348 0.000114 0.000056 0.000037 0.000023 0.000017 0.000014 0.000012 0.00001 0.000008 0.000007 0.180733 1 ## HISTOGRAM java.lang.Integer coverage high_quality_coverage_count 0 1514002365 1 391986260 2 105911639 3 33599419 4 14332156 5 7811853 6 4808908 7 3141265 8 2091176 9 1413221 10 957706 11 660571 12 465187 13 328212 14 234688 15 165169 16 119452 17 89145 18 65072 19 48808 20 37290 21 28924 22 22631 23 16998 24 13367 25 11623 26 9816 27 7693 28 6534 29 5221 30 4539 31 4312 32 3609 33 3250 34 2656 35 2569 36 2303 37 2155 38 1822 39 1482 40 1274 41 1375 42 1418 43 1446 44 1049 45 1065 46 998 47 1022 48 947 49 978 50 904 51 846 52 736 53 637 54 635 55 736 56 668 57 597 58 507 59 531 60 581 61 533 62 498 63 564 64 489 65 419 66 486 67 464 68 325 69 326 70 338 71 372 72 362 73 368 74 450 75 339 76 376 77 384 78 389 79 323 80 415 81 363 82 303 83 325 84 304 85 297 86 292 87 310 88 285 89 285 90 283 91 221 92 249 93 282 94 190 95 177 96 212 97 243 98 180 99 197 100 214 101 252 102 217 103 156 104 226 105 173 106 201 107 189 108 165 109 175 110 150 111 157 112 164 113 147 114 178 115 242 116 169 117 177 118 169 119 142 120 103 121 138 122 157 123 136 124 106 125 101 126 115 127 115 128 118 129 109 130 97 131 96 132 90 133 86 134 67 135 73 136 68 137 111 138 70 139 66 140 74 141 64 142 48 143 63 144 46 145 58 146 64 147 101 148 67 149 79 150 98 151 99 152 76 153 61 154 68 155 89 156 80 157 65 158 57 159 54 160 46 161 45 162 52 163 53 164 52 165 70 166 65 167 103 168 62 169 76 170 72 171 73 172 85 173 83 174 68 175 58 176 39 177 50 178 55 179 40 180 68 181 62 182 80 183 63 184 60 185 64 186 43 187 55 188 53 189 39 190 55 191 33 192 39 193 47 194 39 195 45 196 22 197 42 198 31 199 37 200 54 201 44 202 30 203 37 204 37 205 37 206 34 207 29 208 27 209 27 210 35 211 29 212 33 213 30 214 29 215 36 216 46 217 31 218 34 219 36 220 36 221 21 222 33 223 31 224 38 225 37 226 34 227 27 228 23 229 24 230 25 231 27 232 25 233 22 234 31 235 28 236 40 237 29 238 24 239 29 240 39 241 22 242 35 243 34 244 30 245 29 246 34 247 29 248 25 249 24 250 4562