## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT 659_djb-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_djb-T1-TRNA-1_B23MHV2LT4_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: Fri May 22 22:11:24 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 72409376550 71571042174 8870 65306069487 4635088922 1431824670 198050225 0 0 0 12324019 234648112 1169978 0.0499 0.9501 0 0.912465 0.064762 0.020006 0.002767 0.977227 0.965913 0 0.595445 0.444946 0.735994 0.668648 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.272717 1 0.300595 2 0.344146 3 0.404033 4 0.457078 5 0.50355 6 0.553586 7 0.595029 8 0.649235 9 0.688731 10 0.724841 11 0.765885 12 0.823997 13 0.879515 14 0.92302 15 0.96053 16 0.989178 17 1.011865 18 1.025647 19 1.041095 20 1.058493 21 1.077312 22 1.096563 23 1.102581 24 1.111078 25 1.118721 26 1.12812 27 1.135131 28 1.147507 29 1.157242 30 1.167993 31 1.170521 32 1.167338 33 1.171433 34 1.16377 35 1.163428 36 1.156353 37 1.154123 38 1.151277 39 1.141682 40 1.136288 41 1.13879 42 1.145091 43 1.139767 44 1.137494 45 1.142457 46 1.146862 47 1.156712 48 1.160132 49 1.161837 50 1.171723 51 1.173347 52 1.171528 53 1.167459 54 1.17644 55 1.180252 56 1.178143 57 1.178831 58 1.165959 59 1.155157 60 1.15663 61 1.164165 62 1.165326 63 1.159782 64 1.151597 65 1.144002 66 1.134455 67 1.131972 68 1.129327 69 1.129525 70 1.126331 71 1.120343 72 1.115305 73 1.112894 74 1.111063 75 1.109693 76 1.106164 77 1.0996 78 1.096984 79 1.088573 80 1.074558 81 1.061623 82 1.045011 83 1.024772 84 1.012927 85 0.99623 86 0.971321 87 0.95793 88 0.940264 89 0.918287 90 0.896889 91 0.865379 92 0.843201 93 0.815012 94 0.78694 95 0.750318 96 0.710681 97 0.668766 98 0.624607 99 0.576926 100 0.528063