## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=WTM_1_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/WTM_1_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 10:53:18 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 1275585450 1275408293 275373742 587160192 173371570 71996760 167506029 0 0 0 16845 9834963 15031 0.00171 0.99829 0.21591 0.46037 0.135934 0.05645 0.131335 0.596305 0.596222 0 0.703371 0.040025 0.68656 0.064261 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.036217 1 0.045272 2 0.076018 3 0.131203 4 0.188428 5 0.280611 6 0.387794 7 0.481297 8 0.558074 9 0.607781 10 0.640621 11 0.666373 12 0.730354 13 0.771721 14 0.812389 15 0.84677 16 0.859688 17 0.886429 18 0.907628 19 0.936823 20 0.97424 21 1.002394 22 1.020332 23 1.038309 24 1.047909 25 1.065369 26 1.078117 27 1.119554 28 1.131058 29 1.129709 30 1.153838 31 1.15619 32 1.1662 33 1.174737 34 1.188225 35 1.202218 36 1.204265 37 1.207841 38 1.19955 39 1.211153 40 1.226025 41 1.224345 42 1.236011 43 1.238562 44 1.230317 45 1.220302 46 1.210295 47 1.191466 48 1.186704 49 1.204899 50 1.206012 51 1.183836 52 1.184796 53 1.203143 54 1.212464 55 1.211373 56 1.197391 57 1.185261 58 1.21896 59 1.251391 60 1.25517 61 1.221781 62 1.177649 63 1.184081 64 1.188556 65 1.194439 66 1.165231 67 1.143094 68 1.134886 69 1.129878 70 1.13121 71 1.146401 72 1.149375 73 1.139733 74 1.12328 75 1.101417 76 1.09426 77 1.114335 78 1.118096 79 1.114673 80 1.104699 81 1.082341 82 1.069061 83 1.068339 84 1.0658 85 1.082724 86 1.078586 87 1.077295 88 1.094084 89 1.084411 90 1.06769 91 1.064954 92 1.054133 93 1.009074 94 0.962434 95 0.923313 96 0.873806 97 0.769754 98 0.582588 99 0.338139 100 0.112541