## 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_00176_23KKJ7LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00176_23KKJ7LT4_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: Thu Mar 05 23:03:49 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 23740368692 22637391897 285942 14137405006 2542193601 5137413571 820093777 0 0 0 3506171 49055112 364568 0.066706 0.933294 0.000013 0.624516 0.112301 0.226944 0.036227 0.736816 0.702584 0 0.677598 0.460719 0.503879 1.073804 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.32635 1 0.380741 2 0.462215 3 0.534331 4 0.599784 5 0.665943 6 0.727874 7 0.788554 8 0.845859 9 0.900254 10 0.9546 11 1.003695 12 1.046047 13 1.087316 14 1.119521 15 1.131446 16 1.120432 17 1.13176 18 1.130479 19 1.135727 20 1.141254 21 1.150799 22 1.166242 23 1.176279 24 1.18782 25 1.196945 26 1.200443 27 1.195859 28 1.196095 29 1.179559 30 1.171233 31 1.164748 32 1.163252 33 1.161162 34 1.152204 35 1.152407 36 1.153458 37 1.152815 38 1.149133 39 1.161381 40 1.179514 41 1.187835 42 1.188873 43 1.191489 44 1.183819 45 1.172622 46 1.167871 47 1.171895 48 1.163552 49 1.161273 50 1.144844 51 1.143244 52 1.141611 53 1.128574 54 1.135345 55 1.120733 56 1.10052 57 1.089378 58 1.089787 59 1.086545 60 1.087882 61 1.095922 62 1.097383 63 1.083203 64 1.077838 65 1.072432 66 1.068149 67 1.059799 68 1.052044 69 1.048201 70 1.035345 71 1.027179 72 1.026009 73 1.021169 74 1.007944 75 0.998817 76 0.99311 77 0.992903 78 0.981197 79 0.968638 80 0.961883 81 0.953598 82 0.938016 83 0.918598 84 0.908204 85 0.898272 86 0.887701 87 0.875584 88 0.849783 89 0.818446 90 0.792177 91 0.773617 92 0.742709 93 0.708095 94 0.685873 95 0.663413 96 0.637969 97 0.611485 98 0.572336 99 0.535034 100 0.543858