## 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_00136_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00136_B23WHTKLT4_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: Thu May 21 06:02:02 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 68785090233 68088713683 2906 61121446187 4774396235 1934682613 258185742 0 0 0 7635132 209976582 991465 0.035086 0.964914 0 0.897674 0.07012 0.028414 0.003792 0.967794 0.957996 0 0.502709 0.490061 0.776776 0.709312 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.302083 1 0.339805 2 0.387198 3 0.441462 4 0.500633 5 0.5573 6 0.605565 7 0.645257 8 0.692065 9 0.734208 10 0.773565 11 0.810936 12 0.849652 13 0.886791 14 0.918431 15 0.947233 16 0.97047 17 0.988393 18 1.003985 19 1.017985 20 1.035236 21 1.052377 22 1.071726 23 1.086807 24 1.092603 25 1.100096 26 1.107535 27 1.113642 28 1.117785 29 1.11661 30 1.116392 31 1.123628 32 1.126118 33 1.13548 34 1.136501 35 1.142217 36 1.142817 37 1.139803 38 1.138621 39 1.135489 40 1.13204 41 1.150171 42 1.140316 43 1.141645 44 1.148823 45 1.152702 46 1.14551 47 1.150147 48 1.14672 49 1.144076 50 1.15192 51 1.154193 52 1.155085 53 1.156527 54 1.156369 55 1.161623 56 1.170733 57 1.170959 58 1.167378 59 1.162356 60 1.159336 61 1.158298 62 1.153264 63 1.145678 64 1.138923 65 1.130272 66 1.128034 67 1.126819 68 1.128332 69 1.122853 70 1.123051 71 1.12968 72 1.133213 73 1.136632 74 1.119838 75 1.111369 76 1.099459 77 1.088929 78 1.084427 79 1.073934 80 1.059941 81 1.048047 82 1.039336 83 1.027673 84 1.013133 85 0.994473 86 0.974013 87 0.96514 88 0.946779 89 0.926485 90 0.904966 91 0.87971 92 0.858117 93 0.829937 94 0.801315 95 0.772569 96 0.740627 97 0.70309 98 0.657501 99 0.616023 100 0.574945