## 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_00166_23KMKGLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00166_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 23:38:09 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 24358289193 23982202708 12470 21337945523 1595385913 933932723 114926079 0 0 0 1406020 77275802 273708 0.01787 0.98213 0.000001 0.889741 0.066524 0.038943 0.004792 0.956265 0.9415 0 0.60136 0.518327 0.672277 0.909853 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.291264 1 0.331069 2 0.386755 3 0.45328 4 0.511931 5 0.563326 6 0.626617 7 0.688812 8 0.7484 9 0.806829 10 0.862584 11 0.915181 12 0.964698 13 1.007564 14 1.044022 15 1.073592 16 1.094493 17 1.115838 18 1.121935 19 1.127307 20 1.142782 21 1.160413 22 1.185594 23 1.20325 24 1.211281 25 1.209211 26 1.205506 27 1.207794 28 1.218678 29 1.215745 30 1.214091 31 1.206893 32 1.202218 33 1.196131 34 1.186868 35 1.186112 36 1.184572 37 1.176017 38 1.1642 39 1.154239 40 1.146145 41 1.145138 42 1.148984 43 1.146722 44 1.143243 45 1.149071 46 1.147449 47 1.149952 48 1.158563 49 1.161394 50 1.161505 51 1.16072 52 1.158265 53 1.155319 54 1.157011 55 1.154285 56 1.151385 57 1.148365 58 1.141776 59 1.132429 60 1.128873 61 1.124277 62 1.123894 63 1.1137 64 1.104044 65 1.100871 66 1.098207 67 1.092911 68 1.086263 69 1.078196 70 1.068733 71 1.056273 72 1.051093 73 1.041919 74 1.027992 75 1.017852 76 1.007054 77 1.001805 78 0.998158 79 0.994093 80 0.985714 81 0.971035 82 0.956185 83 0.942222 84 0.924859 85 0.912299 86 0.892258 87 0.879474 88 0.859935 89 0.840151 90 0.818944 91 0.78792 92 0.764418 93 0.736729 94 0.706025 95 0.678479 96 0.649126 97 0.620117 98 0.58457 99 0.547431 100 0.505594