## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT NTC_0001_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT NTC_0001_0001_B23LG7FLT4_2_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: Tue Mar 03 22:04:42 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 341866160 1584361 10228 147103 52955 882040 492035 0 0 0 233 587 6 0.284146 0.715854 0.006456 0.092847 0.033424 0.556717 0.310557 0.12627 0.000585 0 2.434436 0 0 0 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.386544 1 0.820578 2 0.884067 3 0.884067 4 0.884067 5 0.884067 6 0.884067 7 0.938234 8 0.715054 9 0.645717 10 0.645717 11 0.645717 12 0.457007 13 0.354214 14 0.237937 15 0.318954 16 0.441726 17 0.514045 18 1.091645 19 1.125193 20 1.083866 21 0.891587 22 0.514197 23 0.514634 24 0.514634 25 0.514634 26 0.553625 27 0.70959 28 1.017426 29 1.182338 30 1.094768 31 0.887943 32 0.898445 33 0.991096 34 0.772196 35 0.838966 36 0.844839 37 0.844619 38 0.872719 39 0.993719 40 0.823001 41 1.491911 42 1.960146 43 1.590092 44 0.938145 45 0.897978 46 0.77474 47 0.726063 48 0.667872 49 0.79046 50 0.877603 51 0.942322 52 0.963359 53 1.075676 54 1.143955 55 1.390536 56 1.764803 57 2.118063 58 1.999694 59 1.608697 60 1.622295 61 1.698695 62 1.788553 63 1.478708 64 1.429642 65 1.67342 66 1.669885 67 1.53917 68 1.838603 69 1.695923 70 1.439945 71 1.306669 72 1.207805 73 1.227016 74 1.166242 75 1.062807 76 0.729506 77 0.752099 78 0.694209 79 0.628231 80 0.626939 81 0.617889 82 0.575006 83 0.568879 84 0.547345 85 0.4526 86 0.690363 87 1.28676 88 1.507157 89 1.47624 90 1.422424 91 1.086714 92 1.01343 93 0.982203 94 0.982203 95 0.943782 96 0.881938 97 0.945633 98 0.892153 99 0.892153 100 0.834236