## 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-6473fb-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-6473fb-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 23:33:02 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 23954438827 23638050574 2292 21478332427 1410271981 646257448 103186426 0 0 0 2540729 77044311 502793 0.031925 0.968075 0 0.908634 0.059661 0.02734 0.004365 0.968295 0.955506 0 0.625535 0.40144 0.667162 0.653732 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.26861 1 0.298879 2 0.345213 3 0.405471 4 0.464041 5 0.520424 6 0.575868 7 0.622272 8 0.67185 9 0.714847 10 0.750822 11 0.783838 12 0.829098 13 0.867333 14 0.90087 15 0.932889 16 0.956922 17 0.983705 18 0.996388 19 1.013112 20 1.03075 21 1.046711 22 1.065113 23 1.080709 24 1.094929 25 1.103478 26 1.109535 27 1.115059 28 1.126844 29 1.132376 30 1.138341 31 1.141102 32 1.142311 33 1.142112 34 1.146051 35 1.152689 36 1.155945 37 1.161208 38 1.172388 39 1.17024 40 1.169353 41 1.177146 42 1.182442 43 1.18965 44 1.192937 45 1.192862 46 1.181487 47 1.179317 48 1.174705 49 1.181708 50 1.195461 51 1.19289 52 1.189892 53 1.19614 54 1.192098 55 1.184952 56 1.182861 57 1.173199 58 1.17213 59 1.176158 60 1.181612 61 1.186468 62 1.190804 63 1.172581 64 1.164546 65 1.15893 66 1.145044 67 1.134966 68 1.134607 69 1.135546 70 1.134642 71 1.127564 72 1.120085 73 1.111594 74 1.108163 75 1.104122 76 1.097808 77 1.091508 78 1.081777 79 1.064281 80 1.049855 81 1.037074 82 1.020536 83 1.007039 84 0.995415 85 0.98098 86 0.966713 87 0.956468 88 0.937848 89 0.916431 90 0.882674 91 0.850618 92 0.82026 93 0.786348 94 0.756831 95 0.732999 96 0.699758 97 0.662042 98 0.620207 99 0.580235 100 0.541398