## htsjdk.samtools.metrics.StringHeader # picard.analysis.CollectWgsMetrics INPUT=/gscratch/scrubbed/strigg/analyses/20200613/16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=16C_32psu_2_S2_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 23:18:41 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 0.464414 1.25591 0 0 0.196738 0 0 0.014487 0.342647 0.000889 0.554761 0.284418 0.010304 0.001621 0.0004 0.000144 0.00007 0.000043 0.000026 0.00002 0.000016 0.000014 0.000013 0.000012 0.000011 0.193076 1 ## HISTOGRAM java.lang.Integer coverage high_quality_coverage_count 0 1490177971 1 402608670 2 116178021 3 37177054 4 14869377 5 7541594 6 4462043 7 2880951 8 1899099 9 1298947 10 898999 11 630273 12 454328 13 323795 14 235473 15 171388 16 129195 17 99307 18 74886 19 57878 20 45619 21 36207 22 29782 23 23136 24 19276 25 15577 26 12818 27 10426 28 9274 29 7831 30 6010 31 5500 32 4547 33 4071 34 3398 35 2890 36 2465 37 2296 38 2419 39 2112 40 1730 41 1646 42 1665 43 1458 44 1285 45 1154 46 1182 47 972 48 903 49 769 50 971 51 757 52 985 53 808 54 723 55 754 56 684 57 581 58 523 59 520 60 503 61 520 62 417 63 393 64 368 65 402 66 368 67 320 68 350 69 395 70 353 71 326 72 325 73 280 74 385 75 316 76 251 77 270 78 204 79 211 80 253 81 193 82 227 83 178 84 239 85 260 86 209 87 195 88 222 89 213 90 244 91 207 92 156 93 227 94 234 95 175 96 235 97 215 98 228 99 190 100 202 101 230 102 192 103 213 104 235 105 211 106 233 107 222 108 243 109 233 110 232 111 267 112 142 113 146 114 119 115 124 116 152 117 148 118 139 119 122 120 172 121 159 122 154 123 141 124 157 125 140 126 146 127 215 128 156 129 135 130 128 131 139 132 147 133 116 134 106 135 144 136 164 137 150 138 154 139 97 140 109 141 105 142 78 143 101 144 108 145 105 146 98 147 145 148 111 149 143 150 126 151 113 152 111 153 106 154 93 155 83 156 107 157 83 158 75 159 77 160 96 161 95 162 83 163 106 164 96 165 112 166 141 167 99 168 119 169 131 170 104 171 105 172 113 173 117 174 89 175 104 176 100 177 118 178 103 179 100 180 90 181 104 182 114 183 86 184 110 185 99 186 85 187 122 188 92 189 85 190 97 191 88 192 83 193 117 194 105 195 91 196 85 197 106 198 75 199 65 200 75 201 83 202 72 203 70 204 46 205 58 206 66 207 46 208 53 209 72 210 60 211 69 212 62 213 56 214 63 215 67 216 59 217 47 218 58 219 49 220 57 221 67 222 54 223 63 224 109 225 63 226 78 227 73 228 52 229 65 230 56 231 57 232 75 233 55 234 56 235 72 236 62 237 63 238 78 239 66 240 59 241 63 242 46 243 63 244 71 245 57 246 64 247 49 248 58 249 56 250 6496