## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_3.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_3_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: Mon Mar 09 17:59:52 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 25019144485 24715306399 12738 21342848756 2171767950 1006604462 194072493 0 0 0 3695352 75702972 307292 0.046542 0.953458 0.000001 0.863548 0.087871 0.040728 0.007852 0.951419 0.939865 0 0.55299 0.625168 0.67201 0.945888 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.289782 1 0.331912 2 0.39756 3 0.473706 4 0.551995 5 0.627792 6 0.700197 7 0.76996 8 0.833195 9 0.893833 10 0.942585 11 0.992605 12 1.0374 13 1.075643 14 1.100182 15 1.12506 16 1.143674 17 1.155891 18 1.163547 19 1.178152 20 1.191336 21 1.204648 22 1.216047 23 1.219377 24 1.223761 25 1.226037 26 1.22876 27 1.225241 28 1.222789 29 1.214592 30 1.20835 31 1.202788 32 1.186624 33 1.18311 34 1.179994 35 1.174598 36 1.167122 37 1.159007 38 1.14914 39 1.143156 40 1.136747 41 1.135597 42 1.13851 43 1.134642 44 1.129721 45 1.135516 46 1.129832 47 1.123574 48 1.120759 49 1.119923 50 1.120985 51 1.11814 52 1.115952 53 1.115057 54 1.118179 55 1.115539 56 1.110302 57 1.103004 58 1.100136 59 1.098337 60 1.098147 61 1.108475 62 1.11202 63 1.103654 64 1.097746 65 1.095353 66 1.092544 67 1.08686 68 1.079477 69 1.073146 70 1.063823 71 1.055139 72 1.054522 73 1.044142 74 1.033874 75 1.024976 76 1.013654 77 0.994096 78 0.983714 79 0.977734 80 0.963639 81 0.945601 82 0.929948 83 0.911364 84 0.896759 85 0.890053 86 0.874656 87 0.856246 88 0.83406 89 0.812851 90 0.794652 91 0.774745 92 0.757527 93 0.732628 94 0.699088 95 0.666068 96 0.633976 97 0.598394 98 0.561096 99 0.520546 100 0.475482