## htsjdk.samtools.metrics.StringHeader # picard.analysis.CollectWgsMetrics INPUT=/gscratch/scrubbed/strigg/analyses/20200613/CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=CTRL_16C_26psu_1_S19_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 00:34:02 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 0.438592 1.363462 0 0 0.210571 0 0 0.015092 0.334382 0.000444 0.560488 0.23922 0.015815 0.003462 0.000909 0.00028 0.000111 0.000058 0.000028 0.000019 0.000014 0.000011 0.000009 0.000008 0.000007 0.162824 1 ## HISTOGRAM java.lang.Integer coverage high_quality_coverage_count 0 1584300793 1 338298737 2 83641927 3 28706448 4 14587435 5 9237318 6 6333095 7 4501377 8 3268074 9 2383912 10 1755530 11 1307141 12 974212 13 727329 14 551559 15 417195 16 323096 17 244291 18 186180 19 140239 20 109646 21 83317 22 66157 23 51985 24 41380 25 32732 26 25897 27 20723 28 16744 29 13972 30 11315 31 10182 32 7779 33 6612 34 5872 35 5659 36 4647 37 3793 38 3476 39 3112 40 2951 41 2595 42 2162 43 2210 44 1955 45 1778 46 1599 47 1472 48 1241 49 1170 50 1307 51 1083 52 851 53 910 54 770 55 975 56 699 57 717 58 676 59 754 60 770 61 753 62 729 63 710 64 617 65 539 66 512 67 506 68 551 69 471 70 525 71 461 72 481 73 459 74 464 75 389 76 336 77 419 78 480 79 424 80 437 81 314 82 315 83 276 84 255 85 279 86 299 87 255 88 281 89 239 90 254 91 216 92 230 93 214 94 195 95 156 96 162 97 211 98 222 99 288 100 189 101 199 102 213 103 206 104 212 105 181 106 179 107 144 108 140 109 129 110 92 111 160 112 150 113 130 114 173 115 164 116 118 117 128 118 86 119 108 120 153 121 93 122 164 123 138 124 113 125 122 126 84 127 115 128 101 129 104 130 100 131 143 132 110 133 111 134 98 135 116 136 94 137 90 138 77 139 97 140 99 141 83 142 64 143 69 144 62 145 72 146 93 147 74 148 101 149 79 150 69 151 60 152 68 153 64 154 89 155 69 156 82 157 94 158 70 159 61 160 56 161 50 162 65 163 65 164 101 165 63 166 52 167 52 168 44 169 35 170 36 171 52 172 55 173 39 174 34 175 36 176 45 177 39 178 38 179 45 180 36 181 58 182 50 183 45 184 35 185 30 186 36 187 40 188 40 189 34 190 46 191 41 192 35 193 44 194 45 195 42 196 43 197 28 198 33 199 36 200 41 201 31 202 30 203 41 204 32 205 40 206 37 207 27 208 33 209 40 210 30 211 28 212 25 213 15 214 23 215 18 216 19 217 14 218 21 219 30 220 23 221 23 222 16 223 14 224 15 225 12 226 27 227 22 228 26 229 16 230 17 231 18 232 21 233 21 234 25 235 29 236 23 237 24 238 43 239 23 240 26 241 15 242 18 243 16 244 25 245 20 246 19 247 25 248 26 249 25 250 4366