## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_15.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_15_rna_metrics.txt --TMP_DIR ./tmp --MINIMUM_LENGTH 500 --RRNA_FRAGMENT_PERCENTAGE 0.8 --METRIC_ACCUMULATION_LEVEL ALL_READS --END_BIAS_BASES 100 --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 --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false ## htsjdk.samtools.metrics.StringHeader # Started on: Mon Mar 09 17:59:23 GMT 2026 ## 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 25289335687 24992531902 8974 21572393182 2064257824 1212743368 143128554 0 0 0 4019696 75377219 300695 0.050628 0.949372 0 0.863154 0.082595 0.048524 0.005727 0.945749 0.934649 0 0.522778 0.566632 0.76009 0.826286 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.280146 1 0.317634 2 0.371537 3 0.4326 4 0.497604 5 0.563361 6 0.626725 7 0.687315 8 0.739396 9 0.790224 10 0.834885 11 0.883414 12 0.93076 13 0.966398 14 0.992096 15 1.017434 16 1.042006 17 1.061691 18 1.077705 19 1.09441 20 1.106058 21 1.121901 22 1.136122 23 1.150472 24 1.157564 25 1.160194 26 1.165989 27 1.174115 28 1.181945 29 1.182236 30 1.180946 31 1.182009 32 1.173377 33 1.171287 34 1.168198 35 1.165517 36 1.163541 37 1.155919 38 1.14659 39 1.140071 40 1.129471 41 1.120567 42 1.122373 43 1.125373 44 1.123998 45 1.134004 46 1.133042 47 1.129936 48 1.129856 49 1.136138 50 1.141235 51 1.138718 52 1.135671 53 1.13528 54 1.136111 55 1.139604 56 1.142776 57 1.143068 58 1.140306 59 1.139553 60 1.137769 61 1.144046 62 1.142956 63 1.135039 64 1.132139 65 1.13322 66 1.128062 67 1.123384 68 1.116532 69 1.108797 70 1.097961 71 1.091912 72 1.091365 73 1.083631 74 1.078647 75 1.072927 76 1.061246 77 1.044686 78 1.037528 79 1.028392 80 1.011715 81 0.995692 82 0.988793 83 0.97396 84 0.962691 85 0.955819 86 0.943322 87 0.927305 88 0.907533 89 0.889583 90 0.866577 91 0.84261 92 0.819653 93 0.789546 94 0.757064 95 0.72485 96 0.687631 97 0.650255 98 0.613409 99 0.573987 100 0.530255