## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_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: Thu May 28 22:48:54 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 76622868748 75715249872 10966 66327913145 7054609989 2023681412 309034360 0 0 0 2943155 236211073 1579125 0.012307 0.987693 0 0.876018 0.093173 0.026728 0.004082 0.969191 0.95771 0 0.551954 0.581538 0.699391 0.9033 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.259136 1 0.302447 2 0.370295 3 0.44168 4 0.516013 5 0.594867 6 0.674094 7 0.742671 8 0.80423 9 0.8607 10 0.909582 11 0.961258 12 1.011681 13 1.059159 14 1.092837 15 1.119298 16 1.140316 17 1.153225 18 1.165141 19 1.180307 20 1.194844 21 1.210039 22 1.225481 23 1.234733 24 1.240614 25 1.242196 26 1.245885 27 1.250565 28 1.243524 29 1.23817 30 1.228674 31 1.220295 32 1.197847 33 1.19446 34 1.190504 35 1.191924 36 1.189749 37 1.175276 38 1.15987 39 1.157179 40 1.149651 41 1.147062 42 1.14792 43 1.149333 44 1.150289 45 1.160114 46 1.159205 47 1.155104 48 1.148532 49 1.149469 50 1.152039 51 1.150902 52 1.144653 53 1.144731 54 1.148217 55 1.148406 56 1.143757 57 1.138941 58 1.13118 59 1.125151 60 1.122737 61 1.122917 62 1.115594 63 1.103966 64 1.094172 65 1.086352 66 1.082021 67 1.076373 68 1.065579 69 1.055418 70 1.045381 71 1.035109 72 1.028957 73 1.017508 74 1.010287 75 0.999634 76 0.988787 77 0.968935 78 0.960874 79 0.956937 80 0.928128 81 0.907144 82 0.897729 83 0.885387 84 0.872732 85 0.86004 86 0.845898 87 0.842329 88 0.831332 89 0.812077 90 0.796165 91 0.774782 92 0.755734 93 0.733192 94 0.70632 95 0.674702 96 0.641379 97 0.607742 98 0.56967 99 0.532217 100 0.495696