## htsjdk.samtools.metrics.StringHeader # picard.analysis.CollectWgsMetrics INPUT=/gscratch/scrubbed/strigg/analyses/20200613/16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=16C_26psu_3_S15_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 22:58:04 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 0.323927 0.879185 0 0 0.251227 0 0 0.015551 0.286789 0.00015 0.553718 0.229787 0.003015 0.000324 0.000125 0.000069 0.000045 0.000032 0.00002 0.000014 0.000011 0.000008 0.000007 0.000006 0.000005 0.146868 1 ## HISTOGRAM java.lang.Integer coverage high_quality_coverage_count 0 1603945300 1 354583863 2 86269949 3 23685288 4 7706097 5 2994705 6 1341789 7 675082 8 371521 9 221186 10 144550 11 100869 12 73252 13 54816 14 41052 15 33155 16 25560 17 21517 18 18765 19 15892 20 13783 21 11261 22 9621 23 8613 24 7064 25 6902 26 5727 27 5049 28 4524 29 4273 30 3612 31 3525 32 3274 33 2905 34 2849 35 2621 36 2142 37 2026 38 2056 39 1852 40 1679 41 1577 42 1414 43 1339 44 1187 45 1171 46 1007 47 1056 48 1103 49 891 50 806 51 806 52 581 53 503 54 480 55 494 56 484 57 472 58 518 59 549 60 552 61 493 62 471 63 548 64 570 65 518 66 538 67 496 68 457 69 374 70 403 71 334 72 339 73 357 74 390 75 364 76 399 77 308 78 285 79 281 80 264 81 294 82 259 83 256 84 278 85 227 86 244 87 217 88 236 89 191 90 229 91 161 92 197 93 153 94 160 95 170 96 189 97 197 98 180 99 135 100 123 101 121 102 102 103 108 104 98 105 144 106 132 107 125 108 136 109 159 110 176 111 160 112 130 113 94 114 111 115 109 116 120 117 126 118 122 119 105 120 82 121 117 122 83 123 93 124 80 125 103 126 104 127 102 128 87 129 95 130 93 131 70 132 64 133 68 134 67 135 68 136 82 137 65 138 74 139 68 140 87 141 64 142 57 143 59 144 55 145 50 146 66 147 62 148 65 149 48 150 50 151 41 152 40 153 45 154 44 155 27 156 43 157 47 158 39 159 45 160 58 161 63 162 52 163 40 164 52 165 46 166 57 167 47 168 61 169 44 170 55 171 48 172 37 173 45 174 33 175 36 176 34 177 21 178 36 179 40 180 36 181 47 182 33 183 22 184 31 185 25 186 32 187 26 188 21 189 24 190 23 191 11 192 13 193 14 194 15 195 22 196 23 197 16 198 36 199 28 200 31 201 20 202 18 203 28 204 30 205 28 206 29 207 25 208 27 209 18 210 29 211 23 212 27 213 24 214 24 215 27 216 16 217 21 218 24 219 15 220 22 221 31 222 23 223 49 224 46 225 35 226 37 227 26 228 26 229 19 230 24 231 18 232 25 233 18 234 21 235 23 236 9 237 16 238 17 239 29 240 41 241 18 242 30 243 25 244 21 245 26 246 21 247 19 248 25 249 18 250 2133