## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT LungN_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT LungN_FFPE_L01_RNA_01_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 21:25:48 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 66322799368 65216085290 27764 57286089385 5006649913 2517496981 405821247 0 0 0 20003542 219739550 1254935 0.083437 0.916563 0 0.878404 0.07677 0.038602 0.006223 0.955174 0.939236 0 0.673495 0.442057 0.620908 0.76102 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.265646 1 0.298886 2 0.352521 3 0.41618 4 0.48153 5 0.546652 6 0.613889 7 0.677035 8 0.745382 9 0.796523 10 0.844443 11 0.892404 12 0.934373 13 0.969903 14 0.998465 15 1.026575 16 1.042268 17 1.054724 18 1.074322 19 1.090933 20 1.095873 21 1.101274 22 1.119113 23 1.12976 24 1.137374 25 1.145904 26 1.147692 27 1.151866 28 1.161327 29 1.159856 30 1.157966 31 1.153058 32 1.142011 33 1.144171 34 1.140481 35 1.148855 36 1.150599 37 1.148869 38 1.140103 39 1.131415 40 1.127049 41 1.130566 42 1.140679 43 1.158977 44 1.173613 45 1.192033 46 1.200911 47 1.207769 48 1.20229 49 1.20237 50 1.193703 51 1.185894 52 1.182757 53 1.188278 54 1.185315 55 1.180123 56 1.172601 57 1.158082 58 1.157112 59 1.150558 60 1.146029 61 1.151201 62 1.154044 63 1.143545 64 1.141729 65 1.137272 66 1.126863 67 1.116401 68 1.113118 69 1.108471 70 1.096807 71 1.079549 72 1.073792 73 1.058771 74 1.051271 75 1.048652 76 1.046897 77 1.038036 78 1.032361 79 1.026721 80 1.01983 81 1.011756 82 1.003136 83 0.990268 84 0.974599 85 0.950979 86 0.925027 87 0.907133 88 0.889573 89 0.870214 90 0.840088 91 0.804455 92 0.776909 93 0.74897 94 0.724323 95 0.698814 96 0.668074 97 0.642246 98 0.605082 99 0.565324 100 0.524646