## 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-573e21-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-573e21-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 20:16:01 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 74386384789 73585410287 3006 67173945680 4530258303 1583915502 297287796 0 0 0 5555287 247141186 1306585 0.021984 0.978016 0 0.91287 0.061565 0.021525 0.00404 0.974435 0.963943 0 0.555486 0.563273 0.679313 0.935212 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.312419 1 0.351427 2 0.407847 3 0.477668 4 0.541188 5 0.599003 6 0.65688 7 0.710086 8 0.77249 9 0.824149 10 0.876895 11 0.929539 12 0.982104 13 1.024836 14 1.054915 15 1.073353 16 1.097001 17 1.123817 18 1.138444 19 1.155971 20 1.170466 21 1.182282 22 1.195089 23 1.205406 24 1.212223 25 1.213477 26 1.215463 27 1.214444 28 1.215527 29 1.218416 30 1.2099 31 1.199478 32 1.183589 33 1.181714 34 1.178796 35 1.179622 36 1.177567 37 1.178696 38 1.185695 39 1.186718 40 1.190117 41 1.190455 42 1.198091 43 1.202715 44 1.195799 45 1.197703 46 1.1901 47 1.187047 48 1.178234 49 1.175733 50 1.16197 51 1.156512 52 1.14653 53 1.141939 54 1.136405 55 1.133987 56 1.127771 57 1.122576 58 1.11885 59 1.111516 60 1.10679 61 1.10827 62 1.113019 63 1.096039 64 1.091038 65 1.084771 66 1.07883 67 1.065833 68 1.057965 69 1.051762 70 1.043735 71 1.035459 72 1.031811 73 1.023705 74 1.013125 75 1.001661 76 0.995824 77 0.986473 78 0.982652 79 0.97612 80 0.96312 81 0.950487 82 0.938688 83 0.928283 84 0.915508 85 0.901481 86 0.87669 87 0.858625 88 0.836189 89 0.815045 90 0.796078 91 0.778967 92 0.749151 93 0.718824 94 0.68676 95 0.658772 96 0.635301 97 0.609788 98 0.577313 99 0.546777 100 0.510124