## 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-a03f86-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-a03f86-R1_B23WHYVLT4_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: Thu May 14 23:37:22 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 25806220289 25527022435 1120 23110442862 1586159088 747838952 82580413 0 0 0 1419846 81669872 582274 0.017088 0.982912 0 0.905332 0.062136 0.029296 0.003235 0.967469 0.957002 0 0.552111 0.504728 0.738715 0.754985 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.298369 1 0.328856 2 0.369065 3 0.421198 4 0.467938 5 0.512926 6 0.570449 7 0.620325 8 0.667165 9 0.712448 10 0.756635 11 0.802113 12 0.846669 13 0.8855 14 0.91733 15 0.946148 16 0.96929 17 0.991003 18 1.009734 19 1.026719 20 1.043359 21 1.065268 22 1.088758 23 1.113214 24 1.126936 25 1.13466 26 1.141681 27 1.149174 28 1.159841 29 1.166005 30 1.173331 31 1.176829 32 1.179798 33 1.189266 34 1.184153 35 1.184808 36 1.188778 37 1.185064 38 1.187287 39 1.181052 40 1.179099 41 1.180858 42 1.184585 43 1.194683 44 1.197719 45 1.210044 46 1.211678 47 1.214048 48 1.208176 49 1.210545 50 1.208959 51 1.203707 52 1.198012 53 1.190776 54 1.187056 55 1.175227 56 1.17025 57 1.165059 58 1.159255 59 1.148427 60 1.139431 61 1.141889 62 1.143872 63 1.143381 64 1.147495 65 1.15167 66 1.138692 67 1.120564 68 1.115403 69 1.109851 70 1.098268 71 1.088251 72 1.083007 73 1.081778 74 1.079331 75 1.076913 76 1.059708 77 1.044962 78 1.04163 79 1.031972 80 1.023081 81 1.010713 82 0.994723 83 0.983067 84 0.972494 85 0.962073 86 0.942982 87 0.929263 88 0.909971 89 0.894051 90 0.871153 91 0.845256 92 0.815681 93 0.778592 94 0.74747 95 0.720527 96 0.689714 97 0.660503 98 0.623779 99 0.583214 100 0.543511