## 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-38a0a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-38a0a3-R1_A23WJ53LT4_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: Tue May 19 21:25:02 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 75878725273 75116782526 876 68708717130 4429949975 1804923439 173191106 0 0 0 6982266 242796225 1328753 0.027954 0.972046 0 0.914692 0.058974 0.024028 0.002306 0.973666 0.963889 0 0.51612 0.503479 0.703022 0.783482 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.290247 1 0.325503 2 0.373045 3 0.430941 4 0.486862 5 0.537719 6 0.592986 7 0.646189 8 0.703615 9 0.755237 10 0.800106 11 0.84669 12 0.892409 13 0.931146 14 0.965363 15 1.001614 16 1.02984 17 1.055194 18 1.072818 19 1.094258 20 1.11398 21 1.131562 22 1.147956 23 1.163031 24 1.175328 25 1.178145 26 1.174484 27 1.179069 28 1.185463 29 1.184111 30 1.183616 31 1.181021 32 1.172191 33 1.172215 34 1.167358 35 1.175089 36 1.175382 37 1.176061 38 1.176693 39 1.175882 40 1.16948 41 1.170728 42 1.176238 43 1.18607 44 1.188582 45 1.194957 46 1.18666 47 1.185602 48 1.183283 49 1.179245 50 1.181802 51 1.175287 52 1.165166 53 1.166654 54 1.170378 55 1.175077 56 1.173037 57 1.169207 58 1.159041 59 1.15166 60 1.142842 61 1.137744 62 1.141617 63 1.12981 64 1.128508 65 1.123815 66 1.117967 67 1.110226 68 1.107663 69 1.102377 70 1.092954 71 1.081938 72 1.075889 73 1.075142 74 1.066525 75 1.056854 76 1.049005 77 1.041783 78 1.035913 79 1.025666 80 1.010248 81 0.993306 82 0.979384 83 0.96325 84 0.94296 85 0.925974 86 0.905431 87 0.892617 88 0.871591 89 0.84932 90 0.827796 91 0.809198 92 0.780775 93 0.749225 94 0.720507 95 0.691708 96 0.663536 97 0.631326 98 0.595929 99 0.562551 100 0.529317