## 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_39.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_39_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 17:59:49 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 24769578537 24472319934 30770 21164163889 2002661544 1167322559 138141172 0 0 0 1884297 77330367 326207 0.023787 0.976213 0.000001 0.86482 0.081834 0.0477 0.005645 0.946654 0.935293 0 0.537093 0.54329 0.754305 0.811199 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.283831 1 0.318281 2 0.365286 3 0.420469 4 0.484241 5 0.548318 6 0.610197 7 0.671911 8 0.723734 9 0.772047 10 0.816852 11 0.86564 12 0.912644 13 0.952217 14 0.981556 15 1.006751 16 1.032128 17 1.052871 18 1.066104 19 1.08351 20 1.098425 21 1.118582 22 1.135221 23 1.148739 24 1.15767 25 1.16346 26 1.171169 27 1.18105 28 1.18909 29 1.189145 30 1.184584 31 1.184313 32 1.17556 33 1.170936 34 1.166985 35 1.166243 36 1.164958 37 1.156336 38 1.145196 39 1.142062 40 1.134723 41 1.129476 42 1.132333 43 1.133999 44 1.128256 45 1.13507 46 1.133551 47 1.128753 48 1.128053 49 1.13547 50 1.139574 51 1.139043 52 1.137752 53 1.141269 54 1.146075 55 1.1478 56 1.147114 57 1.147319 58 1.144673 59 1.141906 60 1.143081 61 1.146923 62 1.14721 63 1.141665 64 1.139244 65 1.140159 66 1.135063 67 1.130395 68 1.122547 69 1.11442 70 1.104206 71 1.098851 72 1.09818 73 1.089247 74 1.083247 75 1.076252 76 1.063963 77 1.045941 78 1.03705 79 1.02709 80 1.013428 81 0.995886 82 0.989764 83 0.978101 84 0.966044 85 0.95969 86 0.945039 87 0.926814 88 0.907028 89 0.889125 90 0.867595 91 0.843429 92 0.819657 93 0.791228 94 0.759219 95 0.72576 96 0.690109 97 0.654926 98 0.619368 99 0.580844 100 0.535211