## htsjdk.samtools.metrics.StringHeader # picard.analysis.CollectWgsMetrics INPUT=/gscratch/scrubbed/strigg/analyses/20200613/8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=8C_26psu_1_S9_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 23:40:04 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 0.503495 1.246073 0 0 0.209941 0 0 0.0148 0.318355 0.00069 0.543785 0.315054 0.00954 0.001246 0.000288 0.000107 0.000058 0.000039 0.000026 0.000021 0.000017 0.000015 0.000013 0.000012 0.000011 0.207129 1 ## HISTOGRAM java.lang.Integer coverage high_quality_coverage_count 0 1426379401 1 442969319 2 134616336 3 42548096 4 16089116 5 7642771 6 4278356 7 2593651 8 1668849 9 1087910 10 737132 11 503221 12 342815 13 239638 14 171671 15 125651 16 90144 17 68055 18 53695 19 40454 20 31755 21 23939 22 18342 23 15289 24 12919 25 10884 26 8348 27 7137 28 6254 29 5538 30 4648 31 3550 32 3495 33 3192 34 2773 35 2480 36 2202 37 2048 38 1684 39 1571 40 1678 41 1634 42 1271 43 1187 44 1052 45 910 46 889 47 926 48 791 49 686 50 870 51 709 52 639 53 641 54 709 55 798 56 750 57 690 58 754 59 605 60 612 61 514 62 507 63 410 64 413 65 472 66 362 67 345 68 360 69 360 70 386 71 422 72 403 73 394 74 450 75 427 76 420 77 305 78 307 79 386 80 332 81 294 82 305 83 291 84 248 85 261 86 257 87 208 88 269 89 211 90 182 91 169 92 170 93 210 94 227 95 147 96 153 97 160 98 152 99 174 100 181 101 188 102 196 103 187 104 229 105 151 106 132 107 148 108 176 109 163 110 139 111 205 112 126 113 125 114 140 115 150 116 133 117 157 118 164 119 162 120 219 121 185 122 158 123 173 124 157 125 169 126 166 127 146 128 151 129 152 130 178 131 182 132 148 133 142 134 134 135 119 136 114 137 123 138 107 139 113 140 133 141 109 142 137 143 121 144 165 145 147 146 158 147 138 148 159 149 137 150 144 151 120 152 196 153 141 154 117 155 118 156 124 157 118 158 130 159 117 160 116 161 118 162 107 163 96 164 114 165 106 166 110 167 116 168 110 169 101 170 96 171 97 172 98 173 97 174 95 175 104 176 109 177 119 178 91 179 92 180 98 181 119 182 113 183 108 184 118 185 101 186 133 187 102 188 93 189 91 190 86 191 99 192 107 193 98 194 106 195 114 196 104 197 95 198 95 199 98 200 86 201 77 202 75 203 75 204 90 205 73 206 78 207 84 208 84 209 81 210 59 211 57 212 69 213 53 214 60 215 75 216 75 217 74 218 60 219 55 220 67 221 76 222 84 223 64 224 76 225 59 226 59 227 49 228 66 229 34 230 41 231 50 232 59 233 68 234 65 235 53 236 60 237 47 238 49 239 46 240 49 241 62 242 59 243 76 244 75 245 65 246 55 247 54 248 64 249 61 250 7084