## 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-3377ac-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-3377ac-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 20:17:54 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 70099568881 69277243238 6448 63382596531 3910755819 1703646217 280238223 0 0 0 12365931 241123050 973623 0.048783 0.951217 0 0.914912 0.056451 0.024592 0.004045 0.971363 0.959968 0 0.573858 0.517182 0.68926 0.839231 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.304646 1 0.33734 2 0.392815 3 0.458387 4 0.519527 5 0.57139 6 0.631091 7 0.689033 8 0.743736 9 0.796808 10 0.845335 11 0.895679 12 0.944559 13 0.987677 14 1.021547 15 1.052768 16 1.077675 17 1.096692 18 1.114892 19 1.129231 20 1.142253 21 1.156823 22 1.173963 23 1.18634 24 1.18931 25 1.194379 26 1.201128 27 1.207641 28 1.213727 29 1.209789 30 1.200609 31 1.192904 32 1.189396 33 1.184264 34 1.167883 35 1.164797 36 1.1653 37 1.160044 38 1.161399 39 1.161305 40 1.158724 41 1.153932 42 1.151938 43 1.153737 44 1.153637 45 1.160685 46 1.156961 47 1.157535 48 1.152639 49 1.153209 50 1.148532 51 1.149217 52 1.150187 53 1.148378 54 1.149465 55 1.145531 56 1.145633 57 1.13655 58 1.131788 59 1.12234 60 1.116449 61 1.115412 62 1.106974 63 1.097468 64 1.102861 65 1.107896 66 1.101193 67 1.092368 68 1.08295 69 1.075301 70 1.068056 71 1.058078 72 1.052307 73 1.047907 74 1.041784 75 1.038762 76 1.029795 77 1.019323 78 1.009592 79 1.000905 80 0.989082 81 0.979362 82 0.970578 83 0.959488 84 0.948862 85 0.93585 86 0.913763 87 0.904885 88 0.888075 89 0.870456 90 0.841073 91 0.812628 92 0.779257 93 0.749896 94 0.720049 95 0.689209 96 0.66014 97 0.626069 98 0.587818 99 0.55016 100 0.514352