## htsjdk.samtools.metrics.StringHeader # picard.analysis.CollectWgsMetrics INPUT=/gscratch/scrubbed/strigg/analyses/20200613/8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=8C_26psu_4_S12_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 00:01:36 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 0.243771 0.696173 0 0 0.284178 0 0 0.015211 0.255817 0.00005 0.555256 0.18337 0.001545 0.000126 0.000056 0.000035 0.000025 0.000018 0.000011 0.000007 0.000005 0.000004 0.000004 0.000003 0.000002 0.113899 1 ## HISTOGRAM java.lang.Integer coverage high_quality_coverage_count 0 1700606242 1 296694989 2 62028522 3 15292391 4 4629578 5 1686347 6 701792 7 320910 8 157013 9 88867 10 54649 11 34340 12 23862 13 18347 14 14186 15 11629 16 9525 17 8488 18 7773 19 6832 20 5090 21 4901 22 4311 23 3605 24 3319 25 2945 26 2907 27 2459 28 2446 29 2259 30 2076 31 1886 32 1772 33 1549 34 1454 35 1500 36 1183 37 1302 38 1199 39 1222 40 1102 41 1043 42 980 43 817 44 841 45 899 46 589 47 624 48 503 49 500 50 440 51 504 52 477 53 429 54 370 55 366 56 354 57 279 58 262 59 300 60 288 61 290 62 308 63 253 64 254 65 211 66 210 67 150 68 176 69 158 70 145 71 167 72 136 73 135 74 161 75 166 76 167 77 234 78 242 79 188 80 142 81 141 82 130 83 103 84 146 85 136 86 138 87 145 88 141 89 138 90 111 91 150 92 119 93 147 94 118 95 152 96 96 97 78 98 81 99 71 100 76 101 83 102 66 103 82 104 81 105 69 106 81 107 86 108 78 109 77 110 77 111 57 112 39 113 46 114 37 115 44 116 84 117 43 118 54 119 56 120 30 121 38 122 40 123 43 124 37 125 34 126 38 127 56 128 74 129 36 130 43 131 38 132 35 133 51 134 37 135 38 136 35 137 25 138 32 139 22 140 24 141 34 142 32 143 42 144 52 145 48 146 51 147 47 148 35 149 31 150 25 151 32 152 29 153 22 154 21 155 17 156 39 157 34 158 21 159 40 160 33 161 19 162 21 163 15 164 17 165 9 166 10 167 17 168 11 169 20 170 26 171 30 172 29 173 17 174 17 175 11 176 11 177 30 178 25 179 13 180 18 181 20 182 20 183 26 184 22 185 16 186 13 187 8 188 6 189 11 190 12 191 9 192 5 193 7 194 9 195 10 196 12 197 11 198 10 199 14 200 12 201 6 202 13 203 11 204 13 205 16 206 22 207 17 208 22 209 27 210 22 211 22 212 27 213 23 214 20 215 16 216 13 217 18 218 37 219 18 220 16 221 11 222 10 223 19 224 14 225 15 226 12 227 10 228 15 229 10 230 21 231 3 232 10 233 8 234 15 235 10 236 9 237 13 238 9 239 18 240 21 241 11 242 11 243 7 244 9 245 9 246 11 247 18 248 13 249 15 250 666