## 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_s29.Aligned.sortedByCoord.out.bam --OUTPUT V4_0001_RNA_0005_23H5VFLT4_s29_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 22:22:12 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 25181496782 24811993967 48078 19472178789 2354854144 2633869463 351043493 0 0 0 2549979 69566692 340251 0.035359 0.964641 0.000002 0.784789 0.094908 0.106153 0.014148 0.879697 0.866789 0 0.517823 0.564636 0.740129 0.84844 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.297338 1 0.337638 2 0.40071 3 0.467302 4 0.533924 5 0.598589 6 0.662273 7 0.721159 8 0.771705 9 0.823792 10 0.863685 11 0.905661 12 0.949533 13 0.987741 14 1.018341 15 1.047094 16 1.070474 17 1.087719 18 1.093561 19 1.106921 20 1.125567 21 1.142682 22 1.159196 23 1.170173 24 1.180568 25 1.184365 26 1.187494 27 1.190797 28 1.192506 29 1.191229 30 1.186691 31 1.186624 32 1.177192 33 1.176355 34 1.169082 35 1.166272 36 1.165328 37 1.156164 38 1.147942 39 1.141552 40 1.134645 41 1.134898 42 1.135939 43 1.13555 44 1.134778 45 1.139246 46 1.136425 47 1.13358 48 1.13644 49 1.137792 50 1.140447 51 1.138069 52 1.134769 53 1.134942 54 1.134982 55 1.135072 56 1.137426 57 1.134426 58 1.131958 59 1.128497 60 1.129981 61 1.136101 62 1.134183 63 1.129515 64 1.128387 65 1.128529 66 1.121357 67 1.114867 68 1.103516 69 1.093789 70 1.082286 71 1.074652 72 1.072234 73 1.063303 74 1.059138 75 1.050145 76 1.038539 77 1.025339 78 1.018027 79 1.005634 80 0.985944 81 0.964182 82 0.953775 83 0.939331 84 0.927796 85 0.920855 86 0.904945 87 0.887111 88 0.86586 89 0.847685 90 0.827866 91 0.808854 92 0.791104 93 0.768359 94 0.742971 95 0.716175 96 0.684815 97 0.650397 98 0.615294 99 0.577806 100 0.534238