## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT dna_s752.Aligned.sortedByCoord.out.bam --OUTPUT dna_s752_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 11:55:14 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 86064659891 85045925238 18483837 32429491472 18907300768 29768913256 3921735905 0 0 0 92626617 91048761 6129783 0.504295 0.495705 0.000217 0.381317 0.222319 0.350033 0.046113 0.603636 0.596491 0 0.374129 0.861422 0.799278 1.02309 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.777289 1 0.833888 2 0.864345 3 0.874127 4 0.873538 5 0.877525 6 0.880614 7 0.882767 8 0.884302 9 0.887352 10 0.889075 11 0.890299 12 0.889236 13 0.895529 14 0.901115 15 0.906559 16 0.907181 17 0.91068 18 0.910732 19 0.919844 20 0.925947 21 0.925424 22 0.926126 23 0.929581 24 0.931971 25 0.940194 26 0.945853 27 0.944892 28 0.947555 29 0.955987 30 0.961922 31 0.96634 32 0.978125 33 0.981979 34 0.981519 35 0.976593 36 0.982957 37 0.988608 38 0.995401 39 1.007238 40 1.015671 41 1.02039 42 1.020145 43 1.024081 44 1.018222 45 1.018473 46 1.023486 47 1.02892 48 1.029295 49 1.027592 50 1.029089 51 1.031397 52 1.036849 53 1.034274 54 1.042744 55 1.045633 56 1.048935 57 1.054437 58 1.061894 59 1.064323 60 1.068299 61 1.072464 62 1.071182 63 1.07436 64 1.075258 65 1.075133 66 1.079655 67 1.082288 68 1.082989 69 1.080765 70 1.083322 71 1.087681 72 1.093922 73 1.102687 74 1.107957 75 1.111124 76 1.112442 77 1.107794 78 1.109884 79 1.113334 80 1.112872 81 1.108606 82 1.100828 83 1.098503 84 1.102079 85 1.098382 86 1.100028 87 1.092426 88 1.08233 89 1.073009 90 1.066481 91 1.058056 92 1.047052 93 1.03579 94 1.016596 95 0.988893 96 0.953494 97 0.915013 98 0.866318 99 0.800375 100 0.737479