## 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_00417_23LGNLLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00417_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: Mon Mar 09 20:02:46 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 24614957118 24260844106 73471 20869294037 1649694416 1545495959 196286223 0 0 0 3606529 75306386 537879 0.045703 0.954297 0.000003 0.860205 0.067998 0.063703 0.008091 0.928203 0.91485 0 0.521029 0.461885 0.787292 0.677182 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.322391 1 0.355751 2 0.398473 3 0.447234 4 0.484007 5 0.516379 6 0.568175 7 0.61402 8 0.659467 9 0.702328 10 0.742585 11 0.775808 12 0.809043 13 0.84455 14 0.873711 15 0.907672 16 0.930574 17 0.958492 18 0.980916 19 0.995825 20 1.008621 21 1.022377 22 1.041796 23 1.058542 24 1.06892 25 1.078091 26 1.087355 27 1.100545 28 1.107243 29 1.104702 30 1.111486 31 1.114029 32 1.117717 33 1.122981 34 1.124266 35 1.131811 36 1.143506 37 1.146911 38 1.151728 39 1.147302 40 1.142801 41 1.142625 42 1.147812 43 1.154825 44 1.161165 45 1.167489 46 1.175393 47 1.177952 48 1.176515 49 1.177804 50 1.17807 51 1.175938 52 1.177435 53 1.173378 54 1.172388 55 1.164292 56 1.15805 57 1.159044 58 1.153013 59 1.145334 60 1.14478 61 1.149438 62 1.149692 63 1.147433 64 1.147531 65 1.145109 66 1.143256 67 1.138004 68 1.131418 69 1.132882 70 1.130177 71 1.123993 72 1.118424 73 1.113523 74 1.105466 75 1.102926 76 1.097299 77 1.090682 78 1.085471 79 1.076718 80 1.070879 81 1.065788 82 1.053574 83 1.038375 84 1.033806 85 1.021621 86 1.004932 87 0.998094 88 0.981555 89 0.961549 90 0.940022 91 0.919536 92 0.885548 93 0.851628 94 0.824055 95 0.794454 96 0.760261 97 0.724976 98 0.687374 99 0.649996 100 0.605056