## htsjdk.samtools.metrics.StringHeader # picard.analysis.CollectWgsMetrics INPUT=/gscratch/scrubbed/strigg/analyses/20200613/8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=8C_32psu_3_S7_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: Wed Jun 17 00:20:39 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 0.357428 1.127476 0 0 0.198803 0 0 0.014383 0.349793 0.000508 0.563487 0.216667 0.010018 0.001537 0.000323 0.000102 0.00005 0.000033 0.000022 0.000017 0.000013 0.000011 0.000009 0.000008 0.000007 0.148557 1 ## HISTOGRAM java.lang.Integer coverage high_quality_coverage_count 0 1631267317 1 318999167 2 74967673 3 24630867 4 11741366 5 6958436 6 4450993 7 2936506 8 1978679 9 1336718 10 922475 11 636352 12 438022 13 311003 14 220051 15 156110 16 113435 17 82546 18 61842 19 46054 20 34965 21 25714 22 20562 23 15293 24 12480 25 10103 26 8161 27 6809 28 5144 29 4808 30 3868 31 3504 32 3245 33 2425 34 2314 35 1914 36 1927 37 1686 38 1655 39 1410 40 1223 41 1179 42 1139 43 1057 44 972 45 1127 46 1115 47 1036 48 996 49 758 50 710 51 752 52 683 53 725 54 655 55 735 56 748 57 630 58 561 59 507 60 484 61 436 62 631 63 467 64 438 65 483 66 452 67 477 68 381 69 377 70 410 71 463 72 428 73 404 74 359 75 379 76 440 77 428 78 359 79 323 80 293 81 277 82 307 83 278 84 261 85 228 86 274 87 257 88 287 89 224 90 199 91 233 92 221 93 196 94 232 95 263 96 196 97 219 98 163 99 167 100 167 101 168 102 170 103 205 104 177 105 174 106 229 107 331 108 163 109 231 110 164 111 151 112 124 113 164 114 130 115 160 116 125 117 104 118 82 119 98 120 95 121 131 122 114 123 111 124 81 125 91 126 102 127 96 128 95 129 97 130 96 131 102 132 92 133 81 134 111 135 83 136 78 137 78 138 100 139 94 140 109 141 84 142 109 143 88 144 86 145 137 146 102 147 93 148 97 149 82 150 79 151 114 152 69 153 87 154 107 155 91 156 98 157 67 158 82 159 83 160 65 161 66 162 56 163 70 164 83 165 61 166 54 167 43 168 45 169 45 170 57 171 57 172 62 173 53 174 58 175 55 176 43 177 38 178 35 179 40 180 32 181 28 182 45 183 41 184 24 185 35 186 26 187 31 188 36 189 56 190 43 191 51 192 47 193 29 194 40 195 42 196 42 197 32 198 24 199 39 200 32 201 30 202 32 203 37 204 49 205 36 206 12 207 39 208 21 209 22 210 24 211 29 212 30 213 20 214 31 215 21 216 24 217 17 218 21 219 30 220 25 221 26 222 10 223 19 224 9 225 13 226 17 227 17 228 25 229 16 230 13 231 21 232 11 233 13 234 19 235 28 236 15 237 17 238 12 239 19 240 14 241 23 242 20 243 19 244 30 245 25 246 29 247 35 248 32 249 41 250 4287