## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-13a2f6-R1_B23WHYVLT4_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 14 23:51:45 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 22519672807 22145912641 6070 20080912231 1360900826 627099113 76994401 0 0 0 2965540 78951744 513249 0.036202 0.963798 0 0.906755 0.061452 0.028317 0.003477 0.968206 0.952137 0 0.637354 0.402024 0.723733 0.516415 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.27785 1 0.302331 2 0.342509 3 0.397111 4 0.443588 5 0.481719 6 0.529636 7 0.569513 8 0.621567 9 0.674765 10 0.720151 11 0.766781 12 0.819244 13 0.862864 14 0.896957 15 0.923463 16 0.947788 17 0.972941 18 0.991332 19 1.009156 20 1.026415 21 1.043089 22 1.055437 23 1.06662 24 1.071988 25 1.082543 26 1.084257 27 1.087913 28 1.101819 29 1.106151 30 1.106056 31 1.115783 32 1.124449 33 1.133057 34 1.131766 35 1.130491 36 1.134316 37 1.137941 38 1.142925 39 1.140531 40 1.136201 41 1.139712 42 1.147332 43 1.147682 44 1.14499 45 1.154987 46 1.159026 47 1.171633 48 1.173592 49 1.179314 50 1.207347 51 1.215797 52 1.222857 53 1.225203 54 1.229003 55 1.221289 56 1.21523 57 1.199066 58 1.180899 59 1.173563 60 1.17282 61 1.166507 62 1.163633 63 1.156919 64 1.157903 65 1.158343 66 1.149538 67 1.144801 68 1.142764 69 1.138352 70 1.129349 71 1.126027 72 1.124558 73 1.123979 74 1.123289 75 1.123122 76 1.119155 77 1.111098 78 1.101718 79 1.089059 80 1.078213 81 1.069526 82 1.059567 83 1.046794 84 1.034689 85 1.014192 86 0.98933 87 0.984892 88 0.973787 89 0.96426 90 0.943615 91 0.911308 92 0.881929 93 0.842519 94 0.806089 95 0.767128 96 0.721258 97 0.686621 98 0.635601 99 0.583292 100 0.535164