## htsjdk.samtools.metrics.StringHeader # picard.analysis.CollectWgsMetrics INPUT=/gscratch/scrubbed/strigg/analyses/20200613/8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=8C_26psu_2_S10_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 23:47:21 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 0.500066 1.289723 0 0 0.198652 0 0 0.0152 0.331185 0.000699 0.545737 0.298529 0.012374 0.002021 0.000453 0.000145 0.000068 0.000042 0.000025 0.000019 0.000016 0.000013 0.000012 0.000011 0.00001 0.198829 1 ## HISTOGRAM java.lang.Integer coverage high_quality_coverage_count 0 1460790789 1 416596615 2 122767792 3 40020269 4 16523797 5 8694420 6 5319594 7 3512413 8 2390716 9 1644041 10 1154031 11 817775 12 578305 13 413295 14 301420 15 219402 16 156535 17 115318 18 85059 19 64797 20 48129 21 38511 22 30823 23 24532 24 19554 25 15820 26 12310 27 10172 28 8531 29 6914 30 5953 31 5548 32 4333 33 3919 34 3259 35 2896 36 2834 37 2220 38 1989 39 1754 40 1659 41 1693 42 1542 43 1489 44 1261 45 1193 46 1097 47 990 48 892 49 958 50 839 51 708 52 654 53 690 54 642 55 591 56 707 57 654 58 673 59 618 60 616 61 516 62 499 63 409 64 530 65 434 66 392 67 385 68 412 69 477 70 481 71 388 72 305 73 313 74 302 75 183 76 196 77 265 78 193 79 213 80 244 81 287 82 259 83 246 84 233 85 268 86 201 87 190 88 184 89 203 90 192 91 236 92 233 93 217 94 218 95 211 96 246 97 198 98 224 99 191 100 222 101 264 102 197 103 212 104 265 105 227 106 190 107 197 108 209 109 191 110 178 111 150 112 153 113 191 114 184 115 159 116 166 117 163 118 168 119 167 120 164 121 196 122 181 123 212 124 184 125 183 126 183 127 173 128 145 129 145 130 137 131 200 132 150 133 173 134 165 135 146 136 128 137 127 138 138 139 131 140 143 141 116 142 144 143 146 144 131 145 135 146 134 147 115 148 104 149 105 150 103 151 108 152 118 153 108 154 98 155 89 156 110 157 115 158 118 159 106 160 107 161 114 162 150 163 132 164 156 165 119 166 121 167 124 168 120 169 113 170 112 171 92 172 79 173 108 174 93 175 99 176 94 177 107 178 94 179 70 180 86 181 73 182 80 183 81 184 67 185 73 186 54 187 76 188 71 189 75 190 79 191 77 192 62 193 73 194 59 195 57 196 48 197 52 198 62 199 58 200 67 201 45 202 50 203 67 204 64 205 73 206 55 207 63 208 54 209 61 210 45 211 54 212 49 213 47 214 42 215 56 216 56 217 52 218 46 219 45 220 56 221 49 222 46 223 39 224 54 225 48 226 61 227 57 228 49 229 35 230 38 231 45 232 52 233 45 234 31 235 30 236 31 237 38 238 43 239 31 240 30 241 31 242 33 243 46 244 32 245 35 246 32 247 39 248 45 249 29 250 5424