## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT tih_rna_sample_00332_23LGNLLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00332_23LGNLLT4_1_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: Tue Mar 10 00:46:51 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 22543462467 21862661683 157258 19360138431 1135240087 1097346689 269779218 0 0 0 2084426 79403819 262931 0.025579 0.974421 0.000007 0.885534 0.051926 0.050193 0.01234 0.93746 0.90915 0 0.856116 0.412001 0.370942 0.913076 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.371164 1 0.408975 2 0.464328 3 0.536838 4 0.609299 5 0.6736 6 0.736493 7 0.802065 8 0.864001 9 0.914854 10 0.97812 11 1.066387 12 1.131403 13 1.176609 14 1.205199 15 1.217125 16 1.213581 17 1.215403 18 1.201966 19 1.205048 20 1.220886 21 1.228271 22 1.25085 23 1.266263 24 1.27669 25 1.285636 26 1.292975 27 1.301379 28 1.302933 29 1.299169 30 1.292922 31 1.294064 32 1.28945 33 1.275572 34 1.255088 35 1.249825 36 1.246546 37 1.226068 38 1.213047 39 1.19895 40 1.197851 41 1.200867 42 1.208561 43 1.218145 44 1.223325 45 1.210614 46 1.199769 47 1.198556 48 1.185145 49 1.16695 50 1.141007 51 1.144287 52 1.146892 53 1.144672 54 1.146401 55 1.1412 56 1.131477 57 1.106762 58 1.093405 59 1.07161 60 1.056491 61 1.059719 62 1.053731 63 1.031956 64 1.014578 65 1.002289 66 0.990681 67 0.98601 68 0.980171 69 0.97277 70 0.954511 71 0.936749 72 0.929685 73 0.926148 74 0.925683 75 0.909189 76 0.897271 77 0.891804 78 0.886012 79 0.86568 80 0.858375 81 0.852269 82 0.852229 83 0.842643 84 0.826153 85 0.811111 86 0.789004 87 0.773866 88 0.755698 89 0.7384 90 0.723978 91 0.705706 92 0.683163 93 0.655716 94 0.628355 95 0.60173 96 0.57483 97 0.548083 98 0.514495 99 0.483786 100 0.450863