## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT V4_0001_RNA_0005_23H5VFLT4_s12.Aligned.sortedByCoord.out.bam --OUTPUT V4_0001_RNA_0005_23H5VFLT4_s12_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: Wed Mar 04 22:55:19 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 25533998285 25149975735 32703 19886279261 2422542516 2471554768 369566487 0 0 0 3511482 69376778 339726 0.048176 0.951824 0.000001 0.790708 0.096324 0.098273 0.014695 0.887032 0.873691 0 0.511863 0.599008 0.732733 0.906176 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.29414 1 0.334981 2 0.402491 3 0.471265 4 0.540601 5 0.607375 6 0.671556 7 0.73369 8 0.790934 9 0.844288 10 0.888238 11 0.935325 12 0.980073 13 1.020362 14 1.052044 15 1.076725 16 1.10028 17 1.116728 18 1.123824 19 1.137505 20 1.15325 21 1.168401 22 1.183488 23 1.19528 24 1.204802 25 1.208416 26 1.21123 27 1.210088 28 1.206637 29 1.202639 30 1.198513 31 1.198207 32 1.185845 33 1.18178 34 1.174572 35 1.170326 36 1.169506 37 1.161575 38 1.153093 39 1.148584 40 1.144976 41 1.14067 42 1.140036 43 1.136585 44 1.132384 45 1.137128 46 1.132475 47 1.126931 48 1.126999 49 1.125824 50 1.127297 51 1.125023 52 1.122116 53 1.121464 54 1.12256 55 1.122695 56 1.123124 57 1.118693 58 1.118903 59 1.115677 60 1.11655 61 1.121024 62 1.116263 63 1.112086 64 1.109958 65 1.110482 66 1.104769 67 1.097967 68 1.088013 69 1.080345 70 1.070751 71 1.06202 72 1.058434 73 1.047741 74 1.042734 75 1.033814 76 1.022367 77 1.007542 78 1.002414 79 0.991355 80 0.972776 81 0.953422 82 0.943081 83 0.928471 84 0.915499 85 0.910771 86 0.895741 87 0.877488 88 0.857958 89 0.839273 90 0.819082 91 0.79931 92 0.781747 93 0.757607 94 0.732601 95 0.704219 96 0.672495 97 0.640304 98 0.606993 99 0.570765 100 0.528297