## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT 659_bUW-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_bUW-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 05:54:57 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 78807269468 78053649295 5463 71725273116 5096060718 1071082862 161227136 0 0 0 9017603 241295684 1155725 0.036025 0.963975 0 0.918923 0.065289 0.013722 0.002066 0.984212 0.9748 0 0.482696 0.552189 0.775682 0.825371 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.243553 1 0.279838 2 0.342751 3 0.411571 4 0.479491 5 0.552211 6 0.60822 7 0.656911 8 0.714154 9 0.766495 10 0.810052 11 0.851832 12 0.895972 13 0.937882 14 0.973731 15 1.005118 16 1.022823 17 1.044545 18 1.055179 19 1.068606 20 1.095603 21 1.116106 22 1.125561 23 1.134591 24 1.144932 25 1.146849 26 1.153404 27 1.153834 28 1.15655 29 1.157977 30 1.159744 31 1.157436 32 1.153298 33 1.155453 34 1.153196 35 1.160544 36 1.161288 37 1.158657 38 1.160704 39 1.160965 40 1.152397 41 1.151714 42 1.153459 43 1.16036 44 1.161171 45 1.173256 46 1.174028 47 1.175194 48 1.172031 49 1.172881 50 1.171811 51 1.1633 52 1.157945 53 1.154159 54 1.161506 55 1.16861 56 1.16741 57 1.16959 58 1.17089 59 1.157356 60 1.1479 61 1.149378 62 1.148569 63 1.144422 64 1.142493 65 1.144581 66 1.143275 67 1.138217 68 1.141392 69 1.138225 70 1.126713 71 1.115926 72 1.108215 73 1.1056 74 1.097652 75 1.087786 76 1.075098 77 1.051063 78 1.044974 79 1.037434 80 1.020136 81 1.008599 82 0.995733 83 0.983506 84 0.971129 85 0.954172 86 0.934938 87 0.915562 88 0.890601 89 0.868649 90 0.84697 91 0.825124 92 0.797524 93 0.765901 94 0.73573 95 0.702014 96 0.668815 97 0.63422 98 0.591401 99 0.553188 100 0.513576