## 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_00087_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00087_B23WHTKLT4_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 21 07:12:06 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 77224640282 76429489988 4353 68849098877 5197970752 2087012327 295403679 0 0 0 9299406 236710813 1200645 0.037801 0.962199 0 0.900819 0.06801 0.027306 0.003865 0.968829 0.958853 0 0.49129 0.526627 0.781139 0.775157 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.297791 1 0.332938 2 0.378914 3 0.435985 4 0.495588 5 0.55786 6 0.613197 7 0.659905 8 0.7127 9 0.772259 10 0.818252 11 0.850982 12 0.889544 13 0.925878 14 0.951719 15 0.976578 16 0.997292 17 1.018989 18 1.034236 19 1.048393 20 1.068186 21 1.090855 22 1.103392 23 1.115824 24 1.126761 25 1.136504 26 1.145316 27 1.148273 28 1.152276 29 1.157059 30 1.156222 31 1.155738 32 1.160704 33 1.164442 34 1.15667 35 1.160234 36 1.162127 37 1.155633 38 1.158713 39 1.156342 40 1.148484 41 1.147575 42 1.146305 43 1.149837 44 1.153359 45 1.152244 46 1.145667 47 1.152651 48 1.157473 49 1.161725 50 1.172874 51 1.178337 52 1.184755 53 1.18705 54 1.187076 55 1.186457 56 1.184645 57 1.172634 58 1.165727 59 1.1644 60 1.162421 61 1.161084 62 1.154826 63 1.144301 64 1.136406 65 1.126211 66 1.115266 67 1.106664 68 1.101762 69 1.093425 70 1.081886 71 1.077744 72 1.073356 73 1.073533 74 1.072977 75 1.062262 76 1.052274 77 1.046968 78 1.048776 79 1.037923 80 1.022403 81 1.009957 82 1.000145 83 0.988814 84 0.979817 85 0.961102 86 0.945079 87 0.93381 88 0.9157 89 0.893477 90 0.868752 91 0.844472 92 0.823742 93 0.798742 94 0.76837 95 0.735107 96 0.703068 97 0.669724 98 0.633477 99 0.597048 100 0.557437