## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT rna_s1221_S42.Aligned.sortedByCoord.out.bam --OUTPUT rna_s1221_S42_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 Jun 03 21:56:51 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 2754287345 2727550835 2380143 2400643463 197498918 94951215 32077096 0 0 0 82025 8016569 44319 0.010128 0.989872 0.000873 0.880146 0.072409 0.034812 0.01176 0.952555 0.943308 0 0.579755 0.568567 0.670525 0.715967 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.31384 1 0.35613 2 0.432987 3 0.515289 4 0.587595 5 0.660486 6 0.726424 7 0.780129 8 0.829338 9 0.872901 10 0.909585 11 0.939608 12 0.975934 13 1.012808 14 1.036853 15 1.064561 16 1.084072 17 1.10147 18 1.109069 19 1.132917 20 1.151881 21 1.16543 22 1.174495 23 1.178809 24 1.186087 25 1.189214 26 1.192396 27 1.188338 28 1.186295 29 1.17864 30 1.160312 31 1.153343 32 1.14244 33 1.147909 34 1.149988 35 1.154553 36 1.15302 37 1.14338 38 1.135031 39 1.12947 40 1.121112 41 1.119347 42 1.12874 43 1.131274 44 1.135245 45 1.133415 46 1.131511 47 1.129232 48 1.12542 49 1.129481 50 1.140017 51 1.13864 52 1.138577 53 1.134826 54 1.137382 55 1.133095 56 1.131532 57 1.128972 58 1.124459 59 1.119512 60 1.114492 61 1.116643 62 1.111405 63 1.105245 64 1.098802 65 1.095564 66 1.094848 67 1.08728 68 1.080188 69 1.078516 70 1.07072 71 1.063914 72 1.056756 73 1.05226 74 1.043466 75 1.036107 76 1.033195 77 1.022765 78 1.01718 79 1.013339 80 0.997186 81 0.981692 82 0.966946 83 0.953471 84 0.935427 85 0.918758 86 0.89125 87 0.878174 88 0.875717 89 0.855333 90 0.837316 91 0.807179 92 0.787559 93 0.76148 94 0.727603 95 0.692064 96 0.655598 97 0.625537 98 0.577016 99 0.535906 100 0.494773