## htsjdk.samtools.metrics.StringHeader # picard.analysis.CollectWgsMetrics INPUT=/gscratch/scrubbed/strigg/analyses/20200613/16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=16C_32psu_3_S3_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 23:26:10 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 0.347545 1.033696 0 0 0.198718 0 0 0.015879 0.351822 0.000382 0.566801 0.223466 0.007326 0.000968 0.000202 0.000072 0.000041 0.00003 0.00002 0.000015 0.000012 0.00001 0.000008 0.000007 0.000006 0.153155 1 ## HISTOGRAM java.lang.Integer coverage high_quality_coverage_count 0 1617107758 1 332920707 2 81691141 3 25052342 4 10440013 5 5558101 6 3322031 7 2095591 8 1364267 9 900927 10 596046 11 404206 12 277180 13 187974 14 129340 15 92549 16 67618 17 49147 18 34971 19 27884 20 19477 21 15295 22 11165 23 9726 24 7774 25 6344 26 4937 27 4606 28 4299 29 3536 30 3187 31 2849 32 2431 33 2038 34 1936 35 1903 36 1733 37 1445 38 1597 39 1203 40 1031 41 1139 42 1077 43 1065 44 878 45 1052 46 958 47 803 48 778 49 841 50 756 51 770 52 734 53 658 54 695 55 660 56 644 57 583 58 518 59 560 60 535 61 548 62 629 63 543 64 493 65 571 66 453 67 404 68 404 69 346 70 293 71 340 72 305 73 296 74 313 75 322 76 312 77 294 78 245 79 309 80 246 81 308 82 248 83 239 84 274 85 248 86 265 87 248 88 228 89 199 90 222 91 277 92 284 93 245 94 237 95 229 96 188 97 194 98 193 99 168 100 243 101 165 102 134 103 109 104 163 105 153 106 122 107 175 108 148 109 186 110 179 111 142 112 104 113 118 114 134 115 155 116 163 117 156 118 193 119 143 120 130 121 114 122 115 123 127 124 95 125 99 126 76 127 94 128 116 129 68 130 73 131 72 132 58 133 83 134 71 135 69 136 139 137 63 138 57 139 58 140 62 141 68 142 49 143 37 144 56 145 54 146 47 147 44 148 49 149 54 150 56 151 65 152 60 153 45 154 65 155 48 156 53 157 40 158 37 159 40 160 47 161 38 162 29 163 39 164 38 165 42 166 47 167 43 168 48 169 32 170 38 171 37 172 38 173 28 174 24 175 36 176 27 177 24 178 27 179 34 180 30 181 35 182 24 183 21 184 22 185 24 186 38 187 41 188 43 189 38 190 36 191 38 192 30 193 51 194 33 195 37 196 38 197 33 198 38 199 33 200 37 201 31 202 31 203 26 204 38 205 48 206 51 207 41 208 31 209 17 210 34 211 27 212 34 213 38 214 45 215 30 216 41 217 61 218 40 219 43 220 52 221 29 222 49 223 28 224 16 225 33 226 34 227 40 228 41 229 41 230 23 231 34 232 25 233 25 234 27 235 30 236 27 237 25 238 19 239 26 240 28 241 20 242 34 243 23 244 25 245 20 246 26 247 24 248 26 249 33 250 3610