## 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-1ffee4-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-1ffee4-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 21:27:01 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 70288261222 69543476475 802 63235436038 4351098748 1764229019 192711868 0 0 0 3697590 224471272 1132055 0.016205 0.983795 0 0.909294 0.062567 0.025369 0.002771 0.97186 0.961562 0 0.501853 0.527412 0.765576 0.766835 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.299112 1 0.334122 2 0.378387 3 0.428767 4 0.475682 5 0.523554 6 0.583801 7 0.635548 8 0.684949 9 0.731088 10 0.777052 11 0.824825 12 0.87091 13 0.91036 14 0.941111 15 0.974292 16 1.004229 17 1.032608 18 1.052928 19 1.064106 20 1.079661 21 1.100407 22 1.12147 23 1.138269 24 1.147292 25 1.157347 26 1.167538 27 1.174314 28 1.180648 29 1.17865 30 1.183143 31 1.183584 32 1.173439 33 1.174645 34 1.170475 35 1.17669 36 1.174093 37 1.168439 38 1.166104 39 1.163253 40 1.159681 41 1.154857 42 1.156473 43 1.159645 44 1.164222 45 1.17639 46 1.174118 47 1.179837 48 1.176875 49 1.176542 50 1.181741 51 1.178224 52 1.172991 53 1.169907 54 1.170637 55 1.172575 56 1.171637 57 1.167866 58 1.160256 59 1.146945 60 1.137747 61 1.135607 62 1.137664 63 1.129002 64 1.13214 65 1.134958 66 1.128775 67 1.121993 68 1.119197 69 1.112974 70 1.100545 71 1.090165 72 1.085401 73 1.082809 74 1.075336 75 1.067939 76 1.058217 77 1.039504 78 1.029848 79 1.021943 80 1.009835 81 0.998209 82 0.991719 83 0.977048 84 0.963836 85 0.952705 86 0.932488 87 0.916992 88 0.895384 89 0.8777 90 0.858869 91 0.840058 92 0.814133 93 0.789288 94 0.758734 95 0.731908 96 0.700659 97 0.6675 98 0.63107 99 0.5955 100 0.560051