## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT 659_bQZ-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_bQZ-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 05:55:48 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 70550828151 69668060294 7410 63013702836 4756875722 1674487775 222986551 0 0 0 12800596 217432407 1076650 0.055598 0.944402 0 0.904485 0.068279 0.024035 0.003201 0.972764 0.960592 0 0.528801 0.51339 0.711217 0.803124 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.285165 1 0.322206 2 0.374159 3 0.433445 4 0.487028 5 0.54052 6 0.602017 7 0.657722 8 0.714997 9 0.765462 10 0.810404 11 0.854388 12 0.901613 13 0.942454 14 0.973079 15 1.001199 16 1.022042 17 1.041802 18 1.057527 19 1.076574 20 1.099321 21 1.119698 22 1.141172 23 1.153399 24 1.163098 25 1.170283 26 1.172694 27 1.177818 28 1.180748 29 1.175032 30 1.165876 31 1.163285 32 1.158234 33 1.164769 34 1.166625 35 1.170532 36 1.173272 37 1.175077 38 1.179783 39 1.180805 40 1.171493 41 1.174995 42 1.183623 43 1.185904 44 1.187598 45 1.185934 46 1.17571 47 1.17029 48 1.168166 49 1.167492 50 1.168673 51 1.159587 52 1.151621 53 1.154713 54 1.164648 55 1.172468 56 1.170823 57 1.162915 58 1.156777 59 1.151495 60 1.149263 61 1.151014 62 1.155096 63 1.151695 64 1.152196 65 1.149998 66 1.148947 67 1.142949 68 1.140562 69 1.1309 70 1.114174 71 1.103308 72 1.093431 73 1.086865 74 1.078296 75 1.071425 76 1.063289 77 1.04523 78 1.034106 79 1.023976 80 1.007773 81 0.990324 82 0.973931 83 0.960462 84 0.940399 85 0.920224 86 0.901093 87 0.887242 88 0.868605 89 0.846462 90 0.824123 91 0.801557 92 0.771453 93 0.741249 94 0.717651 95 0.689384 96 0.659883 97 0.622188 98 0.584603 99 0.550499 100 0.514286