## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT SW780_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT SW780_FFPE_RNA_0001_B23LG7FLT4_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 28 22:49:16 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 74700150076 73792205728 72586 63940782360 5345373920 3910804239 595172623 0 0 0 5855918 231990090 1449650 0.024621 0.975379 0.000001 0.866498 0.072438 0.052998 0.008066 0.938936 0.927524 0 0.504169 0.565626 0.762237 0.799683 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.280742 1 0.311929 2 0.359739 3 0.411741 4 0.474611 5 0.537761 6 0.602023 7 0.663204 8 0.718913 9 0.772102 10 0.821416 11 0.869247 12 0.911068 13 0.952754 14 0.986739 15 1.016826 16 1.046943 17 1.068378 18 1.080553 19 1.094815 20 1.111921 21 1.128479 22 1.138734 23 1.151596 24 1.156107 25 1.159181 26 1.161537 27 1.159296 28 1.156385 29 1.149959 30 1.14478 31 1.14183 32 1.141524 33 1.135682 34 1.127882 35 1.128471 36 1.1312 37 1.124002 38 1.119722 39 1.11688 40 1.118297 41 1.124669 42 1.132025 43 1.139864 44 1.138139 45 1.138829 46 1.129107 47 1.118458 48 1.121069 49 1.130048 50 1.134029 51 1.133442 52 1.141568 53 1.144704 54 1.151188 55 1.152909 56 1.152177 57 1.151768 58 1.146531 59 1.140352 60 1.132782 61 1.132284 62 1.134866 63 1.124832 64 1.120904 65 1.123092 66 1.117451 67 1.110807 68 1.104025 69 1.102608 70 1.101247 71 1.096209 72 1.099216 73 1.100723 74 1.093937 75 1.094797 76 1.089187 77 1.078453 78 1.078825 79 1.072882 80 1.058222 81 1.045115 82 1.033424 83 1.016055 84 1.000502 85 0.989866 86 0.972543 87 0.954872 88 0.931289 89 0.911866 90 0.884784 91 0.858212 92 0.833597 93 0.798217 94 0.761336 95 0.727686 96 0.691247 97 0.657567 98 0.618763 99 0.577699 100 0.531592