## 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_45.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_45_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 17:59:55 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 24572535665 24284540361 14540 20949040959 1993420211 1200658343 141406308 0 0 0 1265506 77880248 325447 0.01599 0.98401 0.000001 0.862649 0.082086 0.049441 0.005823 0.944735 0.933663 0 0.531923 0.547149 0.763857 0.784944 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.278778 1 0.313744 2 0.364944 3 0.424199 4 0.489429 5 0.554544 6 0.617139 7 0.677805 8 0.730591 9 0.780337 10 0.824142 11 0.872626 12 0.91845 13 0.952951 14 0.980493 15 1.00421 16 1.027506 17 1.04509 18 1.059111 19 1.075791 20 1.090968 21 1.111643 22 1.129059 23 1.143953 24 1.152561 25 1.154979 26 1.162809 27 1.170823 28 1.177739 29 1.178633 30 1.176224 31 1.175467 32 1.166494 33 1.165038 34 1.158218 35 1.158033 36 1.158777 37 1.15184 38 1.141354 39 1.137337 40 1.131877 41 1.1303 42 1.131921 43 1.132954 44 1.128208 45 1.136544 46 1.134831 47 1.13204 48 1.133916 49 1.141738 50 1.147494 51 1.146888 52 1.145361 53 1.146267 54 1.149104 55 1.15161 56 1.152552 57 1.150498 58 1.146214 59 1.143519 60 1.14131 61 1.14492 62 1.145034 63 1.139972 64 1.137319 65 1.140411 66 1.136488 67 1.131207 68 1.121447 69 1.113888 70 1.103639 71 1.098676 72 1.098165 73 1.090556 74 1.085958 75 1.080679 76 1.069577 77 1.052114 78 1.04386 79 1.031726 80 1.015836 81 0.999176 82 0.99246 83 0.979825 84 0.969013 85 0.962918 86 0.948523 87 0.93242 88 0.911704 89 0.892718 90 0.868554 91 0.845207 92 0.822083 93 0.791858 94 0.76113 95 0.727982 96 0.691471 97 0.654515 98 0.617259 99 0.578001 100 0.533507