## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT SkinN_FFPE_L09_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT SkinN_FFPE_L09_RNA_01_B23LG7FLT4_1_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: Thu May 28 23:35:01 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 60532185165 58908613975 7249492 48151988859 3618385435 4760779646 2370210543 0 0 0 13617951 193694209 1313859 0.065688 0.934312 0.000123 0.817401 0.061424 0.080816 0.040235 0.878825 0.855254 0 0.814759 0.348267 0.496042 0.77043 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.293902 1 0.327359 2 0.381457 3 0.430485 4 0.478551 5 0.537229 6 0.595841 7 0.640408 8 0.699311 9 0.747753 10 0.784931 11 0.827033 12 0.861844 13 0.895916 14 0.937087 15 0.963813 16 0.979303 17 0.991866 18 1.00871 19 1.028828 20 1.046504 21 1.071867 22 1.082505 23 1.092119 24 1.099776 25 1.111161 26 1.118654 27 1.136051 28 1.156695 29 1.154671 30 1.152708 31 1.157494 32 1.169022 33 1.187456 34 1.18336 35 1.17764 36 1.172967 37 1.174522 38 1.184127 39 1.177103 40 1.169001 41 1.190058 42 1.198713 43 1.197877 44 1.201682 45 1.215418 46 1.214393 47 1.216686 48 1.209167 49 1.199987 50 1.198535 51 1.196583 52 1.195534 53 1.19181 54 1.189726 55 1.178061 56 1.165141 57 1.15533 58 1.145952 59 1.144718 60 1.155558 61 1.158132 62 1.146913 63 1.134234 64 1.129244 65 1.130688 66 1.126603 67 1.115744 68 1.113194 69 1.114188 70 1.1161 71 1.106592 72 1.095276 73 1.088412 74 1.082905 75 1.072883 76 1.074092 77 1.06935 78 1.055346 79 1.040191 80 1.020553 81 1.007327 82 0.99805 83 0.991105 84 0.980479 85 0.97026 86 0.959837 87 0.95317 88 0.93785 89 0.921846 90 0.888661 91 0.854333 92 0.813307 93 0.77323 94 0.724596 95 0.687544 96 0.647911 97 0.612998 98 0.572917 99 0.527617 100 0.483995