## 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_00322_23LGNLLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00322_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 00:24:58 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 24250715759 22404880454 37461 19293065310 1828995614 1045782357 236999712 0 0 0 1338807 72584472 255795 0.018111 0.981889 0.000002 0.86111 0.081634 0.046677 0.010578 0.942744 0.870987 0 0.669312 0.514792 0.518067 1.000894 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.330709 1 0.374874 2 0.447096 3 0.524575 4 0.593528 5 0.656289 6 0.716059 7 0.765784 8 0.819095 9 0.867529 10 0.917929 11 0.959746 12 1.005521 13 1.047757 14 1.07139 15 1.099098 16 1.123741 17 1.140384 18 1.139589 19 1.137146 20 1.149234 21 1.168893 22 1.183737 23 1.194126 24 1.202395 25 1.209707 26 1.217505 27 1.221974 28 1.234466 29 1.244059 30 1.240418 31 1.228964 32 1.22137 33 1.219884 34 1.210194 35 1.210132 36 1.207666 37 1.203999 38 1.202811 39 1.189059 40 1.183829 41 1.182804 42 1.18831 43 1.188535 44 1.183773 45 1.177558 46 1.166132 47 1.162681 48 1.153127 49 1.156933 50 1.150537 51 1.14497 52 1.140521 53 1.132651 54 1.133929 55 1.124701 56 1.118798 57 1.116415 58 1.113637 59 1.111027 60 1.110159 61 1.115023 62 1.112885 63 1.100755 64 1.0917 65 1.088248 66 1.076697 67 1.06503 68 1.059816 69 1.057783 70 1.042204 71 1.030393 72 1.028939 73 1.018828 74 1.017282 75 0.999158 76 0.988607 77 0.97282 78 0.961091 79 0.943845 80 0.934128 81 0.918816 82 0.907518 83 0.888771 84 0.87647 85 0.866571 86 0.849645 87 0.828163 88 0.802688 89 0.779342 90 0.759612 91 0.736765 92 0.721341 93 0.698092 94 0.67311 95 0.648019 96 0.619038 97 0.588699 98 0.556516 99 0.525473 100 0.488837