## 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-714733-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-714733-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 20:18:58 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 75463016653 74601377104 6978 67195666590 4929848750 2201861234 273993552 0 0 0 4000994 246181882 1107309 0.015992 0.984008 0 0.90073 0.066083 0.029515 0.003673 0.966812 0.955773 0 0.532342 0.489822 0.755242 0.754463 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.29683 1 0.329503 2 0.374337 3 0.428139 4 0.476682 5 0.525947 6 0.584671 7 0.639521 8 0.694172 9 0.744887 10 0.789861 11 0.833334 12 0.878094 13 0.921498 14 0.951365 15 0.976508 16 1.006889 17 1.032413 18 1.048479 19 1.065833 20 1.08667 21 1.106361 22 1.128049 23 1.143437 24 1.149887 25 1.155116 26 1.158264 27 1.162592 28 1.170305 29 1.172006 30 1.176513 31 1.182486 32 1.18362 33 1.183425 34 1.180653 35 1.187842 36 1.19635 37 1.193583 38 1.192905 39 1.182953 40 1.179929 41 1.178456 42 1.176073 43 1.180764 44 1.175887 45 1.176903 46 1.174399 47 1.169305 48 1.168558 49 1.167345 50 1.166994 51 1.168861 52 1.169374 53 1.16797 54 1.16225 55 1.158361 56 1.151843 57 1.147501 58 1.137339 59 1.128635 60 1.125685 61 1.129642 62 1.138096 63 1.130306 64 1.135476 65 1.138677 66 1.141855 67 1.138436 68 1.134476 69 1.122271 70 1.105524 71 1.089345 72 1.084702 73 1.083675 74 1.073628 75 1.063339 76 1.053414 77 1.044209 78 1.037123 79 1.023828 80 1.010132 81 0.993609 82 0.981313 83 0.970232 84 0.961135 85 0.947427 86 0.925766 87 0.915656 88 0.898299 89 0.87745 90 0.852812 91 0.838961 92 0.813882 93 0.780018 94 0.743829 95 0.712674 96 0.681916 97 0.649155 98 0.61297 99 0.578856 100 0.541531