## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT tih_rna_sample_00154_23KMKGLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00154_23KMKGLT4_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: Wed Mar 04 23:54:27 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 25258035573 24829476935 19358 21687807220 1798649391 1198037369 144963597 0 0 0 3051524 77234462 333978 0.038008 0.961992 0.000001 0.87347 0.07244 0.048251 0.005838 0.94591 0.929861 0 0.499231 0.58829 0.749379 0.877777 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.331026 1 0.375305 2 0.423269 3 0.479348 4 0.533328 5 0.591956 6 0.651738 7 0.704018 8 0.751014 9 0.803284 10 0.852843 11 0.899847 12 0.949874 13 0.996574 14 1.02839 15 1.05325 16 1.072201 17 1.095491 18 1.110475 19 1.119154 20 1.129776 21 1.130914 22 1.136555 23 1.150284 24 1.157726 25 1.158967 26 1.155015 27 1.159217 28 1.15947 29 1.158256 30 1.160248 31 1.158617 32 1.157186 33 1.159085 34 1.151406 35 1.155859 36 1.149891 37 1.147386 38 1.147585 39 1.14596 40 1.138523 41 1.135937 42 1.137281 43 1.138245 44 1.13612 45 1.150371 46 1.152107 47 1.147151 48 1.141739 49 1.147867 50 1.142428 51 1.137877 52 1.129583 53 1.124592 54 1.125577 55 1.132711 56 1.128778 57 1.127666 58 1.118497 59 1.102575 60 1.097642 61 1.101391 62 1.101672 63 1.096176 64 1.100461 65 1.102126 66 1.097348 67 1.091121 68 1.089447 69 1.086688 70 1.077077 71 1.062013 72 1.055201 73 1.047012 74 1.044839 75 1.048819 76 1.049129 77 1.04405 78 1.041134 79 1.03467 80 1.026049 81 1.012094 82 0.998571 83 0.984852 84 0.975285 85 0.962793 86 0.942149 87 0.930875 88 0.907947 89 0.888698 90 0.866165 91 0.845175 92 0.81956 93 0.78743 94 0.749906 95 0.717633 96 0.683837 97 0.65415 98 0.613522 99 0.57545 100 0.533126