## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT 659_cfy-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_cfy-T1-TRNA-1_B23WHTKLT4_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 21 05:55:54 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 77911922224 77171731373 2936 70668625383 4952332142 1345474319 205296593 0 0 0 14178736 233572837 1130056 0.05723 0.94277 0 0.915732 0.064173 0.017435 0.00266 0.979905 0.970595 0 0.511925 0.495948 0.708657 0.833555 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.267447 1 0.301139 2 0.348962 3 0.404847 4 0.467031 5 0.525171 6 0.580856 7 0.632389 8 0.687351 9 0.736033 10 0.779101 11 0.824135 12 0.874524 13 0.915138 14 0.938699 15 0.967991 16 1.003228 17 1.034564 18 1.056547 19 1.073938 20 1.093725 21 1.116577 22 1.135536 23 1.148623 24 1.158593 25 1.160278 26 1.162788 27 1.163839 28 1.173962 29 1.174113 30 1.177662 31 1.181642 32 1.176137 33 1.180146 34 1.179891 35 1.181537 36 1.18198 37 1.18508 38 1.19545 39 1.197478 40 1.199092 41 1.203686 42 1.208643 43 1.215968 44 1.217795 45 1.217681 46 1.213199 47 1.215203 48 1.213421 49 1.216145 50 1.216261 51 1.207963 52 1.204534 53 1.204113 54 1.206085 55 1.201787 56 1.193601 57 1.190897 58 1.183918 59 1.170791 60 1.169909 61 1.17237 62 1.175835 63 1.164953 64 1.15582 65 1.148407 66 1.147555 67 1.131544 68 1.126456 69 1.119447 70 1.111211 71 1.100907 72 1.094156 73 1.081092 74 1.065017 75 1.054139 76 1.042647 77 1.022819 78 1.012275 79 0.99562 80 0.979154 81 0.963103 82 0.946298 83 0.929172 84 0.913047 85 0.894374 86 0.87114 87 0.854919 88 0.838347 89 0.819135 90 0.805416 91 0.790905 92 0.769915 93 0.745659 94 0.718092 95 0.690535 96 0.663722 97 0.632563 98 0.597223 99 0.566201 100 0.529283