## 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_41.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_41_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 17:59:53 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 25473070713 25191184060 7702 22048465809 2045678621 966175273 130856655 0 0 0 1022546 78942391 345928 0.012787 0.987213 0 0.875245 0.081206 0.038354 0.005195 0.956451 0.945867 0 0.499657 0.589416 0.756094 0.8603 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.264704 1 0.307407 2 0.369343 3 0.438364 4 0.509752 5 0.579517 6 0.643981 7 0.704494 8 0.760106 9 0.813361 10 0.859084 11 0.905277 12 0.953685 13 0.994871 14 1.024687 15 1.051073 16 1.07474 17 1.092087 18 1.108174 19 1.123279 20 1.136627 21 1.149402 22 1.159051 23 1.166675 24 1.174582 25 1.175994 26 1.180529 27 1.184627 28 1.181429 29 1.178065 30 1.172948 31 1.168774 32 1.155808 33 1.153678 34 1.149892 35 1.149018 36 1.153181 37 1.146226 38 1.140595 39 1.140625 40 1.135832 41 1.136558 42 1.139274 43 1.142844 44 1.144228 45 1.153336 46 1.152152 47 1.151695 48 1.150643 49 1.156912 50 1.16443 51 1.16146 52 1.158816 53 1.156207 54 1.155619 55 1.158831 56 1.157108 57 1.155337 58 1.150717 59 1.141416 60 1.135804 61 1.134689 62 1.129579 63 1.124709 64 1.122194 65 1.122652 66 1.119824 67 1.118192 68 1.111964 69 1.104568 70 1.096407 71 1.090764 72 1.086998 73 1.079405 74 1.074888 75 1.063952 76 1.050875 77 1.032506 78 1.025026 79 1.012526 80 0.993575 81 0.97527 82 0.966303 83 0.951254 84 0.93518 85 0.927845 86 0.912662 87 0.893307 88 0.869604 89 0.848505 90 0.830031 91 0.806478 92 0.784753 93 0.755259 94 0.724616 95 0.691007 96 0.658995 97 0.625331 98 0.589746 99 0.551319 100 0.505999