## 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_9.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_9_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 18:00:03 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 25671852182 25381092140 8638 22268117480 2060952737 917637149 134376136 0 0 0 3542817 76687892 303726 0.044158 0.955842 0 0.877351 0.0812 0.036154 0.005294 0.958551 0.947694 0 0.503531 0.605523 0.746336 0.864543 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.266516 1 0.30804 2 0.369615 3 0.440909 4 0.514164 5 0.583543 6 0.648089 7 0.710712 8 0.768421 9 0.822745 10 0.869452 11 0.919343 12 0.970622 13 1.014377 14 1.045931 15 1.073801 16 1.092826 17 1.107731 18 1.121349 19 1.13776 20 1.152882 21 1.168005 22 1.177089 23 1.185459 24 1.191567 25 1.193679 26 1.198813 27 1.202603 28 1.199263 29 1.194327 30 1.188618 31 1.183841 32 1.170476 33 1.164967 34 1.161032 35 1.160786 36 1.161622 37 1.152209 38 1.143339 39 1.140576 40 1.13412 41 1.131639 42 1.133154 43 1.13494 44 1.132574 45 1.141798 46 1.141929 47 1.141057 48 1.140353 49 1.148173 50 1.15708 51 1.157446 52 1.153741 53 1.15267 54 1.151569 55 1.152701 56 1.149313 57 1.146634 58 1.143288 59 1.135115 60 1.131577 61 1.130994 62 1.124619 63 1.117022 64 1.114949 65 1.114793 66 1.113186 67 1.110129 68 1.103097 69 1.094706 70 1.085261 71 1.079269 72 1.074991 73 1.066066 74 1.059843 75 1.052686 76 1.038729 77 1.020388 78 1.012323 79 1.000887 80 0.981715 81 0.961924 82 0.952699 83 0.938922 84 0.925688 85 0.918136 86 0.900539 87 0.882619 88 0.861054 89 0.841572 90 0.825924 91 0.801508 92 0.778811 93 0.750325 94 0.721682 95 0.689042 96 0.655962 97 0.621718 98 0.586747 99 0.549351 100 0.508039