## 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_00017_23LGNLLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00017_23LGNLLT4_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: Sat May 16 09:56:39 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 73970472418 73075685157 42481 63692412472 4694688806 4283299164 405242234 0 0 0 7936354 230357244 1146101 0.033305 0.966695 0.000001 0.871595 0.064244 0.058615 0.005546 0.935839 0.924519 0 0.563415 0.490799 0.716277 0.815545 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.309331 1 0.350661 2 0.405313 3 0.470784 4 0.5245 5 0.571921 6 0.627512 7 0.67952 8 0.734979 9 0.79318 10 0.839625 11 0.879953 12 0.923706 13 0.962981 14 0.998156 15 1.025319 16 1.047898 17 1.06956 18 1.079074 19 1.075601 20 1.081993 21 1.099826 22 1.115774 23 1.133006 24 1.14173 25 1.150512 26 1.155572 27 1.161058 28 1.175812 29 1.186739 30 1.190246 31 1.184739 32 1.18159 33 1.193844 34 1.199593 35 1.210092 36 1.21578 37 1.212709 38 1.207205 39 1.197493 40 1.193288 41 1.194952 42 1.196398 43 1.198088 44 1.19909 45 1.193631 46 1.182972 47 1.178837 48 1.174345 49 1.175018 50 1.170164 51 1.161233 52 1.155893 53 1.151187 54 1.154899 55 1.150605 56 1.151432 57 1.146718 58 1.138306 59 1.130011 60 1.125134 61 1.126169 62 1.120564 63 1.113572 64 1.110309 65 1.10141 66 1.086964 67 1.078968 68 1.069346 69 1.066623 70 1.057993 71 1.048117 72 1.044739 73 1.037954 74 1.025594 75 1.021499 76 1.009767 77 1.003821 78 0.997091 79 0.980642 80 0.972358 81 0.963154 82 0.956181 83 0.944688 84 0.931913 85 0.924087 86 0.917486 87 0.908951 88 0.893113 89 0.872155 90 0.85062 91 0.828126 92 0.805667 93 0.780256 94 0.747582 95 0.71594 96 0.684217 97 0.649364 98 0.615483 99 0.582192 100 0.547706