## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=M2Ezh12F_1_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/M2Ezh12F_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 11:02:24 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 2823600975 2823362062 389866809 1205909082 498088832 243461686 486035653 0 0 0 68221 21975338 53971 0.003095 0.996905 0.138086 0.427118 0.176417 0.086231 0.172148 0.603535 0.603484 0 0.832146 0.033346 0.711804 0.057371 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.032156 1 0.045964 2 0.082236 3 0.14351 4 0.194193 5 0.283171 6 0.378863 7 0.454679 8 0.52007 9 0.58267 10 0.620519 11 0.649922 12 0.718592 13 0.757828 14 0.787039 15 0.800426 16 0.823196 17 0.851504 18 0.88409 19 0.913292 20 0.947698 21 0.966511 22 0.969866 23 0.986072 24 0.992588 25 1.004196 26 1.02215 27 1.061371 28 1.083672 29 1.063082 30 1.082856 31 1.078305 32 1.0907 33 1.100729 34 1.128394 35 1.132826 36 1.151215 37 1.171906 38 1.156951 39 1.157758 40 1.180882 41 1.196042 42 1.20075 43 1.196928 44 1.183867 45 1.168917 46 1.154893 47 1.124504 48 1.122904 49 1.135722 50 1.139521 51 1.129727 52 1.132134 53 1.150819 54 1.171353 55 1.182203 56 1.181272 57 1.188242 58 1.213825 59 1.23881 60 1.241424 61 1.210886 62 1.16935 63 1.168694 64 1.171937 65 1.189577 66 1.17143 67 1.150952 68 1.154784 69 1.14523 70 1.14753 71 1.163272 72 1.15964 73 1.164523 74 1.136203 75 1.121352 76 1.110724 77 1.128557 78 1.139916 79 1.135852 80 1.133611 81 1.135363 82 1.139045 83 1.142099 84 1.153063 85 1.178533 86 1.176175 87 1.168543 88 1.176682 89 1.201762 90 1.168619 91 1.158308 92 1.156775 93 1.131178 94 1.09857 95 1.06769 96 1.020695 97 0.924189 98 0.73302 99 0.465771 100 0.191369