## 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-da06ce-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-da06ce-R1_A23YTGFLT4_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: Wed Jun 03 20:58:54 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 74693009773 73598652817 2938 66105101342 4897980956 2244676617 350890964 0 0 0 18233558 232668084 1282797 0.072672 0.927328 0 0.898184 0.06655 0.030499 0.004768 0.964733 0.950599 0 0.645577 0.577132 0.563869 1.111426 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.360914 1 0.404187 2 0.468974 3 0.541829 4 0.610996 5 0.666408 6 0.727796 7 0.781991 8 0.836292 9 0.88685 10 0.939498 11 0.996505 12 1.046013 13 1.090419 14 1.116996 15 1.145575 16 1.160141 17 1.177079 18 1.191919 19 1.201366 20 1.203394 21 1.214665 22 1.23043 23 1.238324 24 1.246894 25 1.252454 26 1.253789 27 1.250801 28 1.24049 29 1.241905 30 1.239035 31 1.232595 32 1.225256 33 1.215764 34 1.205114 35 1.20714 36 1.20774 37 1.201453 38 1.186547 39 1.171679 40 1.171075 41 1.165218 42 1.163852 43 1.165745 44 1.162944 45 1.164894 46 1.155058 47 1.153502 48 1.144973 49 1.142955 50 1.136712 51 1.137391 52 1.135139 53 1.138531 54 1.136388 55 1.124053 56 1.104349 57 1.085275 58 1.068861 59 1.059997 60 1.05876 61 1.069427 62 1.071031 63 1.058844 64 1.05735 65 1.057441 66 1.058519 67 1.062932 68 1.062714 69 1.053293 70 1.039044 71 1.026872 72 1.020097 73 1.014344 74 1.004536 75 0.995181 76 0.980362 77 0.962393 78 0.945873 79 0.936288 80 0.925565 81 0.914224 82 0.904084 83 0.889304 84 0.872702 85 0.85853 86 0.833364 87 0.814007 88 0.792968 89 0.770107 90 0.748242 91 0.726909 92 0.702045 93 0.67593 94 0.645031 95 0.62146 96 0.599452 97 0.574185 98 0.542515 99 0.518061 100 0.488337