## 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_00501_23LGNLLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00501_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: Sat May 16 10:00:40 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 78885168307 77895091538 60206 66307076251 6232771099 4651309327 703874655 0 0 0 11998608 226240045 1041670 0.050364 0.949636 0.000001 0.851236 0.080015 0.059712 0.009036 0.931251 0.919563 0 0.543553 0.540445 0.729841 0.824209 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.334384 1 0.374433 2 0.425845 3 0.484013 4 0.550762 5 0.61224 6 0.665278 7 0.714954 8 0.771393 9 0.818605 10 0.856505 11 0.894898 12 0.931805 13 0.96296 14 0.984922 15 1.000603 16 1.020277 17 1.043863 18 1.048011 19 1.060132 20 1.078717 21 1.095451 22 1.111248 23 1.118398 24 1.124768 25 1.128302 26 1.134986 27 1.138154 28 1.142627 29 1.147687 30 1.151397 31 1.165102 32 1.18028 33 1.192343 34 1.193905 35 1.191748 36 1.191716 37 1.187397 38 1.182367 39 1.17007 40 1.164844 41 1.165834 42 1.161337 43 1.16388 44 1.165934 45 1.167231 46 1.159571 47 1.144707 48 1.139329 49 1.13667 50 1.135537 51 1.129588 52 1.128908 53 1.13625 54 1.145077 55 1.143465 56 1.141714 57 1.139481 58 1.133247 59 1.130394 60 1.128421 61 1.13054 62 1.129998 63 1.119199 64 1.120814 65 1.126072 66 1.133165 67 1.129886 68 1.122242 69 1.109354 70 1.100951 71 1.08648 72 1.078452 73 1.070902 74 1.060351 75 1.055401 76 1.043938 77 1.029226 78 1.017454 79 1.007056 80 0.993122 81 0.978808 82 0.955979 83 0.936392 84 0.922158 85 0.911537 86 0.897173 87 0.888956 88 0.878622 89 0.860717 90 0.843043 91 0.833073 92 0.811372 93 0.781287 94 0.755391 95 0.733054 96 0.707137 97 0.67621 98 0.644042 99 0.609206 100 0.566311