## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT V4_0001_RNA_0005_23H5VFLT4_s38.Aligned.sortedByCoord.out.bam --OUTPUT V4_0001_RNA_0005_23H5VFLT4_s38_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 22:03:03 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 24687210416 24271510187 91698 18956527969 2365767419 2575468068 373655033 0 0 0 1783379 69504412 348931 0.025017 0.974983 0.000004 0.78102 0.097471 0.106111 0.015395 0.878491 0.863698 0 0.526541 0.550824 0.723429 0.83599 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.290998 1 0.330475 2 0.39486 3 0.461421 4 0.52642 5 0.592941 6 0.657372 7 0.716713 8 0.770415 9 0.826514 10 0.866479 11 0.912832 12 0.959371 13 0.998167 14 1.025932 15 1.052938 16 1.071161 17 1.085147 18 1.089705 19 1.100841 20 1.11746 21 1.135012 22 1.15364 23 1.168146 24 1.179598 25 1.184757 26 1.187207 27 1.187947 28 1.185892 29 1.184306 30 1.181247 31 1.181269 32 1.171185 33 1.172322 34 1.164434 35 1.159111 36 1.160521 37 1.154608 38 1.145079 39 1.140729 40 1.136239 41 1.136279 42 1.137519 43 1.13486 44 1.134799 45 1.143432 46 1.138734 47 1.13483 48 1.134799 49 1.1353 50 1.137967 51 1.135895 52 1.133847 53 1.135221 54 1.135228 55 1.134668 56 1.134327 57 1.130893 58 1.128853 59 1.12678 60 1.129711 61 1.135591 62 1.133416 63 1.126293 64 1.123669 65 1.123437 66 1.118725 67 1.114578 68 1.103402 69 1.096441 70 1.088383 71 1.08092 72 1.078047 73 1.070652 74 1.066601 75 1.056137 76 1.043801 77 1.028461 78 1.018791 79 1.007251 80 0.99223 81 0.972868 82 0.961506 83 0.947214 84 0.933942 85 0.92588 86 0.910044 87 0.891632 88 0.870676 89 0.85036 90 0.82997 91 0.811619 92 0.794019 93 0.771138 94 0.745797 95 0.717516 96 0.685455 97 0.651456 98 0.615409 99 0.575643 100 0.527852