## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=16wk_PBS2_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/16wk_PBS2_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 06:14:26 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 2694902402 2694785185 76193323 1649999055 630274651 133810112 204508044 0 0 0 10906946 10836820 78842 0.501613 0.498387 0.028274 0.612293 0.233887 0.049655 0.07589 0.84618 0.846143 0 0.431204 0.288507 0.262519 1.103887 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.083384 1 0.135838 2 0.235329 3 0.345322 4 0.423868 5 0.517099 6 0.597817 7 0.658495 8 0.712664 9 0.760923 10 0.800984 11 0.839442 12 0.875665 13 0.91154 14 0.939425 15 0.967195 16 0.985663 17 1.006364 18 1.022192 19 1.039332 20 1.059088 21 1.073003 22 1.087119 23 1.097568 24 1.10693 25 1.12288 26 1.131954 27 1.143105 28 1.15511 29 1.164468 30 1.169649 31 1.180656 32 1.189487 33 1.193782 34 1.205009 35 1.216826 36 1.21384 37 1.217117 38 1.222192 39 1.228626 40 1.230494 41 1.235712 42 1.235715 43 1.236105 44 1.233795 45 1.232516 46 1.236781 47 1.237943 48 1.235877 49 1.23323 50 1.236406 51 1.235653 52 1.232122 53 1.231215 54 1.230771 55 1.227547 56 1.22903 57 1.227402 58 1.23048 59 1.231771 60 1.234751 61 1.235212 62 1.228325 63 1.220486 64 1.217567 65 1.21061 66 1.201331 67 1.195375 68 1.191833 69 1.185914 70 1.182005 71 1.179113 72 1.170176 73 1.163273 74 1.153659 75 1.143702 76 1.135941 77 1.12475 78 1.111621 79 1.099307 80 1.0776 81 1.060849 82 1.049438 83 1.031367 84 1.014851 85 0.994866 86 0.970933 87 0.939868 88 0.90255 89 0.856654 90 0.809006 91 0.756115 92 0.700579 93 0.638742 94 0.564743 95 0.478084 96 0.382656 97 0.284927 98 0.186982 99 0.100653 100 0.049989