## htsjdk.samtools.metrics.StringHeader # picard.analysis.CollectWgsMetrics INPUT=/gscratch/scrubbed/strigg/analyses/20200516/Mcap_tg/nodedup/Mcap_RRBS_200M_R1_001_val_1_bismark_bt2_pe.sorted.bam OUTPUT=Mcap_RRBS_200M_R1_001_val_1_bismark_bt2_pe.collect_wgs_metrics.txt REFERENCE_SEQUENCE=/gscratch/srlab/sr320/data/froger/Mcap_Genome/Mcap.genome_assembly.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: Thu May 28 11:50:48 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 885704498 8.864576 39.451881 0 0 0.297143 0 0 0.008838 0.244674 0.130362 0.681016 0.135902 0.079046 0.07233 0.068218 0.064758 0.061595 0.058719 0.053625 0.049302 0.045511 0.042252 0.039412 0.036933 0.034689 0.114497 1 ## HISTOGRAM java.lang.Integer coverage high_quality_coverage_count 0 765335633 1 28962860 2 12468284 3 5848466 4 3078205 5 1872476 6 1308637 7 1037151 8 896858 9 832585 10 782278 11 741708 12 726517 13 708126 14 683363 15 661157 16 633766 17 597445 18 586573 19 585746 20 592268 21 569680 22 556745 23 546975 24 535661 25 532272 26 530751 27 513258 28 490401 29 480544 30 480743 31 474256 32 467075 33 457492 34 457745 35 438356 36 440201 37 434108 38 439427 39 422543 40 408025 41 406155 42 394627 43 391484 44 386936 45 374013 46 370745 47 371682 48 362424 49 362732 50 365823 51 354638 52 352141 53 343674 54 342083 55 328475 56 322923 57 317353 58 321661 59 309351 60 305804 61 296009 62 294998 63 292738 64 295909 65 284358 66 282146 67 280989 68 271410 69 282161 70 266887 71 267291 72 266945 73 255071 74 252262 75 250061 76 247856 77 240981 78 237328 79 231018 80 232651 81 233511 82 226083 83 226728 84 217607 85 212691 86 210172 87 216219 88 211569 89 208298 90 206416 91 212051 92 208410 93 210417 94 199510 95 194065 96 189226 97 188757 98 190320 99 187871 100 188245 101 185603 102 180515 103 177765 104 178342 105 181322 106 169902 107 167693 108 171794 109 167855 110 169678 111 165802 112 164663 113 160682 114 159090 115 157456 116 164278 117 158722 118 157161 119 158699 120 160027 121 157432 122 153684 123 147494 124 145244 125 147331 126 148682 127 149928 128 144240 129 141808 130 141689 131 136961 132 135148 133 131970 134 134784 135 135596 136 127962 137 128473 138 125141 139 126093 140 127745 141 128761 142 127760 143 126693 144 124473 145 120777 146 122004 147 123197 148 118720 149 116913 150 118778 151 116065 152 115695 153 111677 154 112354 155 115908 156 111829 157 111179 158 109996 159 109859 160 110534 161 110865 162 112232 163 107162 164 103751 165 105377 166 101982 167 101905 168 102497 169 103052 170 107942 171 101251 172 105145 173 101151 174 105718 175 98534 176 99521 177 97904 178 99250 179 98803 180 99820 181 98858 182 94584 183 94898 184 93730 185 93509 186 95745 187 93414 188 90303 189 89854 190 87473 191 86878 192 89244 193 87235 194 86977 195 88389 196 86032 197 81792 198 84129 199 83053 200 85423 201 84274 202 83852 203 83565 204 83834 205 83663 206 81940 207 82911 208 78522 209 77758 210 78045 211 79123 212 78307 213 77172 214 72171 215 74588 216 76565 217 75686 218 71612 219 71537 220 73789 221 76926 222 74532 223 77536 224 74185 225 73614 226 73847 227 72253 228 73125 229 72022 230 71083 231 71212 232 71562 233 70403 234 68381 235 67779 236 67223 237 66650 238 68340 239 67881 240 68042 241 68699 242 66853 243 67887 244 66067 245 66171 246 67409 247 62765 248 64559 249 65269 250 14591982