## 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-64fc89-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-64fc89-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 20:55:56 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 75116372940 74298392736 2920 67389108280 4798911198 1911239244 199131094 0 0 0 8337256 234869637 1023528 0.034281 0.965719 0 0.907006 0.06459 0.025724 0.00268 0.971596 0.961016 0 0.536614 0.52114 0.71767 0.81674 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.270687 1 0.309451 2 0.367684 3 0.435879 4 0.504551 5 0.568829 6 0.625927 7 0.67516 8 0.730474 9 0.7829 10 0.830053 11 0.876531 12 0.927555 13 0.980202 14 1.016243 15 1.053522 16 1.077489 17 1.102618 18 1.112636 19 1.118953 20 1.129908 21 1.149727 22 1.168614 23 1.18071 24 1.182431 25 1.187163 26 1.183318 27 1.181934 28 1.182848 29 1.182894 30 1.181133 31 1.184534 32 1.178055 33 1.173008 34 1.16057 35 1.16437 36 1.159524 37 1.15101 38 1.148415 39 1.147106 40 1.136796 41 1.138383 42 1.143236 43 1.143788 44 1.144691 45 1.149998 46 1.146661 47 1.150408 48 1.14676 49 1.143558 50 1.14113 51 1.136668 52 1.129461 53 1.129051 54 1.135015 55 1.140833 56 1.143735 57 1.146026 58 1.141544 59 1.1378 60 1.132043 61 1.132836 62 1.130839 63 1.119327 64 1.108705 65 1.113282 66 1.112968 67 1.108717 68 1.108495 69 1.106058 70 1.095044 71 1.083907 72 1.079273 73 1.081522 74 1.073362 75 1.064587 76 1.053532 77 1.039523 78 1.032126 79 1.027008 80 1.012807 81 0.997757 82 0.98166 83 0.962142 84 0.943048 85 0.925122 86 0.906301 87 0.893023 88 0.874183 89 0.857637 90 0.837131 91 0.82087 92 0.795005 93 0.770226 94 0.740228 95 0.707606 96 0.677981 97 0.651233 98 0.615151 99 0.579036 100 0.541394