## 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_00079_23KKJ7LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00079_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 20:53:44 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 24099628147 22463814469 186429 15431363477 2368940566 3643983043 1019340954 0 0 0 1863593 57990145 447026 0.031136 0.968864 0.000008 0.686943 0.105456 0.162216 0.045377 0.792399 0.738613 0 0.676928 0.524199 0.558273 0.989128 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.36279 1 0.403537 2 0.467944 3 0.539164 4 0.618558 5 0.699316 6 0.761179 7 0.810162 8 0.853923 9 0.891451 10 0.938147 11 0.981516 12 1.02703 13 1.062928 14 1.088784 15 1.103995 16 1.119182 17 1.132643 18 1.1229 19 1.127912 20 1.140549 21 1.15337 22 1.158927 23 1.167406 24 1.179723 25 1.187266 26 1.188382 27 1.184479 28 1.177079 29 1.167872 30 1.162733 31 1.156521 32 1.154971 33 1.155988 34 1.153747 35 1.151288 36 1.146882 37 1.143516 38 1.152294 39 1.142956 40 1.142422 41 1.145876 42 1.152661 43 1.148322 44 1.145733 45 1.155928 46 1.153186 47 1.144617 48 1.138869 49 1.136527 50 1.132897 51 1.126171 52 1.122555 53 1.128918 54 1.136694 55 1.135001 56 1.126587 57 1.117357 58 1.117602 59 1.106318 60 1.094533 61 1.097084 62 1.091508 63 1.084574 64 1.085387 65 1.07928 66 1.076997 67 1.065444 68 1.059296 69 1.056803 70 1.046328 71 1.040362 72 1.042403 73 1.039748 74 1.029856 75 1.021621 76 1.017397 77 1.007085 78 1.00708 79 1.003136 80 0.993623 81 0.9772 82 0.955579 83 0.940893 84 0.929327 85 0.909712 86 0.885335 87 0.86413 88 0.842249 89 0.818302 90 0.794849 91 0.781671 92 0.744785 93 0.714539 94 0.692466 95 0.666873 96 0.642865 97 0.616015 98 0.577672 99 0.545591 100 0.505498