## htsjdk.samtools.metrics.StringHeader # picard.analysis.CollectWgsMetrics INPUT=/gscratch/scrubbed/strigg/analyses/20200613/8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=8C_32psu_2_S6_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 00:14:00 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 0.355911 1.040918 0 0 0.194433 0 0 0.01476 0.341914 0.000617 0.551725 0.233486 0.006917 0.000797 0.000163 0.000062 0.000037 0.000028 0.00002 0.000016 0.000014 0.000012 0.00001 0.000009 0.000008 0.156716 1 ## HISTOGRAM java.lang.Integer coverage high_quality_coverage_count 0 1596240960 1 351534521 2 84420948 3 25329856 4 10538645 5 5531009 6 3231328 7 1965661 8 1229789 9 785830 10 507029 11 333925 12 226160 13 150201 14 102569 15 72384 16 52979 17 37763 18 27210 19 20856 20 15662 21 11985 22 9540 23 7787 24 6180 25 5051 26 4667 27 3535 28 3201 29 2762 30 2628 31 2198 32 2175 33 1451 34 1528 35 1545 36 1379 37 1170 38 1285 39 1109 40 1076 41 880 42 814 43 825 44 832 45 788 46 876 47 863 48 737 49 747 50 643 51 616 52 656 53 638 54 603 55 576 56 500 57 456 58 417 59 422 60 335 61 356 62 366 63 468 64 371 65 347 66 329 67 365 68 466 69 332 70 293 71 305 72 386 73 319 74 282 75 289 76 284 77 264 78 344 79 328 80 281 81 287 82 248 83 240 84 274 85 248 86 224 87 237 88 259 89 263 90 244 91 271 92 259 93 237 94 244 95 218 96 221 97 212 98 234 99 204 100 221 101 200 102 201 103 218 104 219 105 199 106 178 107 188 108 248 109 175 110 161 111 198 112 195 113 191 114 176 115 208 116 169 117 203 118 155 119 140 120 160 121 171 122 128 123 117 124 125 125 146 126 127 127 148 128 106 129 111 130 129 131 113 132 159 133 151 134 104 135 112 136 115 137 112 138 97 139 105 140 111 141 158 142 123 143 97 144 128 145 129 146 104 147 91 148 81 149 78 150 72 151 82 152 92 153 83 154 76 155 55 156 68 157 64 158 83 159 71 160 63 161 66 162 66 163 61 164 69 165 75 166 74 167 66 168 57 169 66 170 72 171 61 172 70 173 58 174 79 175 68 176 68 177 71 178 50 179 71 180 48 181 55 182 52 183 51 184 48 185 60 186 49 187 53 188 58 189 72 190 50 191 48 192 78 193 68 194 45 195 64 196 61 197 46 198 45 199 47 200 46 201 46 202 35 203 39 204 32 205 43 206 52 207 43 208 39 209 43 210 41 211 42 212 52 213 46 214 52 215 33 216 26 217 24 218 34 219 24 220 20 221 31 222 26 223 27 224 27 225 21 226 20 227 13 228 19 229 26 230 30 231 23 232 33 233 18 234 17 235 20 236 37 237 40 238 26 239 28 240 30 241 25 242 28 243 26 244 28 245 21 246 23 247 31 248 32 249 39 250 4305