## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT 659_bNS-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_bNS-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 05:55:53 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 77780834907 76944862038 2102 69864793821 5296016435 1590957792 193091888 0 0 0 12413275 234356351 1196408 0.050303 0.949697 0 0.907985 0.068829 0.020677 0.002509 0.976814 0.966315 0 0.523102 0.545896 0.725479 0.87614 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.265289 1 0.298852 2 0.34497 3 0.405315 4 0.471654 5 0.538253 6 0.596028 7 0.650879 8 0.709349 9 0.758114 10 0.80361 11 0.858504 12 0.918621 13 0.968322 14 0.996315 15 1.029313 16 1.055315 17 1.076286 18 1.098627 19 1.114652 20 1.125846 21 1.142101 22 1.157919 23 1.168031 24 1.170703 25 1.174801 26 1.176997 27 1.180681 28 1.187687 29 1.185889 30 1.181998 31 1.176532 32 1.167983 33 1.168671 34 1.160685 35 1.168438 36 1.17004 37 1.169677 38 1.17072 39 1.16974 40 1.167606 41 1.168434 42 1.180892 43 1.196445 44 1.199228 45 1.210771 46 1.213758 47 1.210313 48 1.204516 49 1.204636 50 1.203087 51 1.199038 52 1.192093 53 1.188431 54 1.185662 55 1.178962 56 1.170349 57 1.168556 58 1.159557 59 1.149499 60 1.143766 61 1.140468 62 1.144119 63 1.13497 64 1.126792 65 1.127016 66 1.122199 67 1.122528 68 1.120262 69 1.110192 70 1.093994 71 1.081106 72 1.072617 73 1.059512 74 1.042503 75 1.035622 76 1.025096 77 1.011183 78 1.006728 79 0.999439 80 0.983415 81 0.970318 82 0.96265 83 0.949155 84 0.92975 85 0.914054 86 0.892289 87 0.876179 88 0.8544 89 0.835607 90 0.818938 91 0.79857 92 0.775327 93 0.748353 94 0.7191 95 0.691123 96 0.659659 97 0.622855 98 0.585154 99 0.548952 100 0.512793