## 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_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_djb-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 05:45:57 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 75854840620 75017973543 4448 68374620050 4827003646 1589918403 226426996 0 0 0 15020538 231209975 978845 0.061002 0.938998 0 0.911443 0.064345 0.021194 0.003018 0.975788 0.965022 0 0.513746 0.472824 0.784141 0.671356 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.301346 1 0.327584 2 0.368923 3 0.419907 4 0.464606 5 0.504904 6 0.552186 7 0.591233 8 0.639334 9 0.679676 10 0.715339 11 0.756069 12 0.808276 13 0.858478 14 0.903165 15 0.939534 16 0.968204 17 0.990235 18 1.004346 19 1.019783 20 1.041086 21 1.058224 22 1.078821 23 1.086475 24 1.095152 25 1.101793 26 1.105797 27 1.107878 28 1.116673 29 1.124208 30 1.131058 31 1.132557 32 1.131963 33 1.141078 34 1.139416 35 1.1463 36 1.143712 37 1.139369 38 1.140159 39 1.138799 40 1.136925 41 1.139956 42 1.144875 43 1.142169 44 1.14329 45 1.147236 46 1.152355 47 1.167807 48 1.175191 49 1.178778 50 1.186504 51 1.18618 52 1.18143 53 1.176177 54 1.176877 55 1.182302 56 1.184883 57 1.186083 58 1.180835 59 1.171447 60 1.169261 61 1.179614 62 1.181775 63 1.178514 64 1.175 65 1.173122 66 1.17457 67 1.174913 68 1.173102 69 1.167569 70 1.154878 71 1.147659 72 1.141091 73 1.138939 74 1.133642 75 1.126601 76 1.120026 77 1.104607 78 1.09987 79 1.090385 80 1.078139 81 1.063188 82 1.053285 83 1.031714 84 1.0175 85 0.999851 86 0.975126 87 0.959463 88 0.937851 89 0.911728 90 0.885364 91 0.857235 92 0.832978 93 0.807138 94 0.774623 95 0.738595 96 0.701364 97 0.662757 98 0.621397 99 0.574779 100 0.531343