## htsjdk.samtools.metrics.StringHeader # picard.analysis.CollectWgsMetrics INPUT=/gscratch/scrubbed/strigg/analyses/20200613/16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=16C_32psu_1_S1_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 23:11:32 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 0.469716 1.400504 0 0 0.196434 0 0 0.014953 0.348558 0.00064 0.560585 0.257032 0.016361 0.003395 0.000826 0.000241 0.000095 0.000053 0.000029 0.000021 0.000017 0.000015 0.000013 0.000011 0.00001 0.177119 1 ## HISTOGRAM java.lang.Integer coverage high_quality_coverage_count 0 1547208113 1 357353181 2 95160389 3 32748113 4 15927599 5 9811952 6 6631452 7 4703338 8 3386823 9 2467193 10 1803988 11 1327095 12 973638 13 715417 14 530984 15 398612 16 297159 17 223858 18 170951 19 127250 20 95733 21 72177 22 57303 23 43738 24 34765 25 26180 26 20622 27 17111 28 13341 29 10315 30 8875 31 7840 32 7063 33 5933 34 5123 35 3947 36 3628 37 2994 38 2642 39 2544 40 2105 41 2063 42 1842 43 1789 44 1401 45 1336 46 1259 47 1188 48 1212 49 1136 50 1125 51 889 52 958 53 777 54 861 55 762 56 858 57 690 58 764 59 622 60 727 61 659 62 585 63 622 64 632 65 609 66 521 67 501 68 377 69 410 70 469 71 467 72 397 73 510 74 438 75 429 76 431 77 377 78 377 79 447 80 441 81 374 82 372 83 330 84 329 85 315 86 431 87 318 88 359 89 285 90 290 91 267 92 252 93 280 94 242 95 232 96 256 97 257 98 296 99 283 100 393 101 303 102 305 103 249 104 273 105 276 106 220 107 211 108 232 109 215 110 237 111 213 112 261 113 235 114 216 115 201 116 233 117 214 118 182 119 217 120 200 121 198 122 279 123 220 124 166 125 278 126 204 127 174 128 158 129 149 130 160 131 176 132 195 133 153 134 155 135 137 136 125 137 119 138 110 139 137 140 111 141 105 142 106 143 102 144 89 145 94 146 85 147 68 148 64 149 64 150 54 151 62 152 61 153 85 154 71 155 80 156 95 157 87 158 49 159 72 160 60 161 64 162 73 163 69 164 63 165 59 166 69 167 70 168 72 169 71 170 64 171 64 172 50 173 61 174 70 175 52 176 44 177 52 178 57 179 64 180 65 181 59 182 58 183 77 184 52 185 74 186 46 187 46 188 54 189 40 190 55 191 36 192 35 193 29 194 51 195 50 196 55 197 49 198 58 199 49 200 45 201 44 202 37 203 32 204 40 205 39 206 37 207 37 208 38 209 35 210 49 211 40 212 38 213 28 214 45 215 32 216 46 217 45 218 31 219 45 220 35 221 30 222 33 223 31 224 25 225 45 226 45 227 43 228 42 229 27 230 25 231 28 232 33 233 28 234 34 235 29 236 25 237 38 238 42 239 35 240 43 241 47 242 32 243 42 244 37 245 38 246 32 247 31 248 15 249 15 250 5829