## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=16wk_ASNase1_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/16wk_ASNase1_metrics MINIMUM_LENGTH=500 RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] ASSUME_SORTED=true STOP_AFTER=0 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 USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader # Started on: Mon Mar 09 06:13:42 EDT 2020 ## METRICS CLASS picard.analysis.RnaSeqMetrics PF_BASES PF_ALIGNED_BASES RIBOSOMAL_BASES CODING_BASES UTR_BASES INTRONIC_BASES INTERGENIC_BASES IGNORED_READS CORRECT_STRAND_READS INCORRECT_STRAND_READS NUM_R1_TRANSCRIPT_STRAND_READS NUM_R2_TRANSCRIPT_STRAND_READS NUM_UNEXPLAINED_READS PCT_R1_TRANSCRIPT_STRAND_READS PCT_R2_TRANSCRIPT_STRAND_READS PCT_RIBOSOMAL_BASES PCT_CODING_BASES PCT_UTR_BASES PCT_INTRONIC_BASES PCT_INTERGENIC_BASES PCT_MRNA_BASES PCT_USABLE_BASES PCT_CORRECT_STRAND_READS MEDIAN_CV_COVERAGE MEDIAN_5PRIME_BIAS MEDIAN_3PRIME_BIAS MEDIAN_5PRIME_TO_3PRIME_BIAS SAMPLE LIBRARY READ_GROUP 2426947887 2426749347 298161767 1344667758 509897020 115932519 158090283 0 0 0 8891988 8824933 66695 0.501892 0.498108 0.122865 0.554102 0.210115 0.047773 0.065145 0.764218 0.764155 0 0.433984 0.27905 0.255903 1.09225 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.082283 1 0.1345 2 0.234778 3 0.344692 4 0.419889 5 0.512405 6 0.595132 7 0.658298 8 0.714053 9 0.760627 10 0.801172 11 0.841773 12 0.881557 13 0.913749 14 0.939355 15 0.967355 16 0.987152 17 1.008949 18 1.026039 19 1.042344 20 1.058578 21 1.073286 22 1.091101 23 1.105629 24 1.115613 25 1.132523 26 1.145512 27 1.155163 28 1.170268 29 1.179606 30 1.185711 31 1.200518 32 1.212627 33 1.215335 34 1.226019 35 1.236852 36 1.23467 37 1.235715 38 1.236574 39 1.238525 40 1.237971 41 1.236619 42 1.231792 43 1.229798 44 1.229568 45 1.230214 46 1.232858 47 1.234528 48 1.234873 49 1.233294 50 1.234805 51 1.23229 52 1.225972 53 1.224192 54 1.223528 55 1.221824 56 1.224093 57 1.22674 58 1.225767 59 1.226708 60 1.228257 61 1.223713 62 1.217015 63 1.214009 64 1.214859 65 1.207937 66 1.198014 67 1.188256 68 1.181204 69 1.173825 70 1.167886 71 1.168188 72 1.162473 73 1.158862 74 1.15246 75 1.142215 76 1.133691 77 1.122866 78 1.113032 79 1.10466 80 1.085129 81 1.067367 82 1.052666 83 1.034859 84 1.013197 85 0.990211 86 0.962367 87 0.930759 88 0.895109 89 0.848352 90 0.799158 91 0.7483 92 0.692388 93 0.628938 94 0.554434 95 0.467695 96 0.373281 97 0.277532 98 0.1816 99 0.096553 100 0.046624