## 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-92d360-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-92d360-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 20:08:54 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 55126782540 54482741964 12694 49495532009 3200908998 1589629196 196659067 0 0 0 6988550 189230412 770438 0.035616 0.964384 0 0.908463 0.058751 0.029177 0.00361 0.967213 0.955914 0 0.567581 0.504957 0.724825 0.742781 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.310351 1 0.337152 2 0.397022 3 0.462781 4 0.510492 5 0.552713 6 0.603959 7 0.646605 8 0.698077 9 0.742783 10 0.786583 11 0.835985 12 0.881411 13 0.917777 14 0.956718 15 0.985764 16 1.011175 17 1.030504 18 1.037785 19 1.053091 20 1.064315 21 1.074112 22 1.091347 23 1.114526 24 1.126311 25 1.130777 26 1.127548 27 1.135695 28 1.145345 29 1.14244 30 1.143453 31 1.150781 32 1.159456 33 1.160885 34 1.149983 35 1.153529 36 1.153613 37 1.150706 38 1.154314 39 1.15963 40 1.157523 41 1.155312 42 1.157709 43 1.164071 44 1.16428 45 1.164227 46 1.160729 47 1.16592 48 1.162768 49 1.16339 50 1.157311 51 1.15553 52 1.155244 53 1.156796 54 1.166982 55 1.167918 56 1.167196 57 1.163716 58 1.154271 59 1.143677 60 1.14201 61 1.146206 62 1.151372 63 1.148954 64 1.163785 65 1.175376 66 1.1686 67 1.164766 68 1.160216 69 1.151467 70 1.147653 71 1.137857 72 1.12782 73 1.11764 74 1.108321 75 1.099079 76 1.079239 77 1.066172 78 1.05407 79 1.038567 80 1.01878 81 1.006404 82 0.994746 83 0.983651 84 0.972006 85 0.957816 86 0.93764 87 0.922596 88 0.903082 89 0.884218 90 0.860243 91 0.840137 92 0.811276 93 0.776845 94 0.738939 95 0.705223 96 0.669355 97 0.632651 98 0.591039 99 0.552466 100 0.51469