## htsjdk.samtools.metrics.StringHeader # picard.analysis.CollectWgsMetrics INPUT=/gscratch/scrubbed/strigg/analyses/20200613/8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=8C_26psu_3_S11_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 23:54:38 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 0.398014 1.239064 0 0 0.199832 0 0 0.01505 0.35613 0.000684 0.571697 0.233746 0.011539 0.002103 0.000525 0.000174 0.000078 0.000046 0.000026 0.000019 0.000016 0.000013 0.000012 0.00001 0.000009 0.16242 1 ## HISTOGRAM java.lang.Integer coverage high_quality_coverage_count 0 1595700075 1 336234071 2 85213461 3 28226662 4 13064182 5 7592697 6 4887365 7 3296892 8 2282232 9 1591520 10 1135016 11 815636 12 585640 13 433313 14 316117 15 233891 16 177301 17 137279 18 104371 19 79069 20 61852 21 46523 22 37310 23 29945 24 23716 25 19139 26 15367 27 12837 28 10467 29 8594 30 7618 31 5926 32 5266 33 4365 34 3915 35 3163 36 2995 37 2917 38 2484 39 2355 40 2069 41 2031 42 1586 43 1542 44 1336 45 1420 46 1347 47 1291 48 1036 49 1125 50 980 51 954 52 696 53 752 54 775 55 584 56 696 57 625 58 624 59 532 60 558 61 552 62 703 63 586 64 454 65 458 66 469 67 393 68 472 69 600 70 404 71 319 72 299 73 390 74 300 75 330 76 347 77 356 78 326 79 359 80 302 81 284 82 346 83 354 84 359 85 340 86 308 87 350 88 288 89 363 90 312 91 400 92 336 93 305 94 267 95 210 96 235 97 190 98 243 99 238 100 224 101 223 102 216 103 222 104 236 105 249 106 221 107 235 108 196 109 206 110 168 111 195 112 164 113 213 114 188 115 187 116 231 117 159 118 177 119 155 120 197 121 185 122 175 123 196 124 176 125 173 126 146 127 135 128 147 129 184 130 137 131 145 132 119 133 140 134 130 135 122 136 141 137 149 138 128 139 123 140 109 141 126 142 111 143 102 144 90 145 103 146 80 147 95 148 88 149 95 150 85 151 147 152 90 153 79 154 68 155 70 156 69 157 73 158 68 159 84 160 76 161 90 162 99 163 134 164 122 165 112 166 89 167 106 168 87 169 80 170 76 171 67 172 67 173 62 174 81 175 65 176 85 177 69 178 65 179 38 180 41 181 42 182 67 183 39 184 57 185 49 186 54 187 42 188 40 189 44 190 85 191 40 192 43 193 32 194 43 195 52 196 46 197 45 198 38 199 27 200 35 201 43 202 31 203 55 204 45 205 45 206 45 207 45 208 52 209 43 210 36 211 32 212 41 213 31 214 58 215 50 216 49 217 47 218 30 219 30 220 24 221 21 222 35 223 34 224 40 225 37 226 61 227 42 228 44 229 36 230 35 231 29 232 34 233 32 234 39 235 27 236 33 237 28 238 32 239 30 240 30 241 37 242 25 243 24 244 17 245 23 246 21 247 23 248 26 249 31 250 5112