## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=2wk_ASNase3_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/2wk_ASNase3_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 06:14:31 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 2782978644 2782863228 45203642 1676276086 670864971 135826025 254692504 0 0 0 11228550 11165448 69743 0.501409 0.498591 0.016244 0.602357 0.24107 0.048808 0.091522 0.843427 0.843392 0 0.447628 0.267004 0.271686 0.936974 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.076206 1 0.122947 2 0.213373 3 0.316455 4 0.387598 5 0.474417 6 0.553978 7 0.616446 8 0.67173 9 0.718445 10 0.758275 11 0.798522 12 0.834709 13 0.867915 14 0.893938 15 0.923488 16 0.945585 17 0.969249 18 0.988069 19 1.003207 20 1.021906 21 1.034146 22 1.049852 23 1.061708 24 1.071806 25 1.08611 26 1.094758 27 1.105614 28 1.120212 29 1.132938 30 1.142563 31 1.156275 32 1.167753 33 1.176294 34 1.178605 35 1.188009 36 1.190102 37 1.196828 38 1.206058 39 1.214937 40 1.221121 41 1.225653 42 1.226444 43 1.226698 44 1.226659 45 1.228191 46 1.232362 47 1.233789 48 1.237886 49 1.24286 50 1.245943 51 1.245516 52 1.242664 53 1.244012 54 1.246182 55 1.245149 56 1.249364 57 1.245559 58 1.242809 59 1.247267 60 1.251841 61 1.250596 62 1.246428 63 1.243342 64 1.24464 65 1.24174 66 1.22889 67 1.217992 68 1.210918 69 1.206579 70 1.20409 71 1.21085 72 1.209461 73 1.206951 74 1.200189 75 1.185095 76 1.170774 77 1.158874 78 1.147398 79 1.138953 80 1.120652 81 1.107546 82 1.09609 83 1.087088 84 1.06733 85 1.044092 86 1.00942 87 0.975867 88 0.936452 89 0.888939 90 0.839351 91 0.787539 92 0.729817 93 0.664224 94 0.586199 95 0.497029 96 0.398415 97 0.293455 98 0.19024 99 0.100788 100 0.04726