## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT FFPE_HD789_02_RNA_0011_23KMKGLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_HD789_02_RNA_0011_23KMKGLT4_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: Sat May 16 11:55:06 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 78450166497 77658984785 41025 69011540033 5377354346 2885385523 384663858 0 0 0 6462456 237575086 1029745 0.026481 0.973519 0.000001 0.888648 0.069243 0.037155 0.004953 0.957892 0.948231 0 0.517936 0.617132 0.732233 0.944963 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.302729 1 0.34803 2 0.403529 3 0.471413 4 0.54645 5 0.617075 6 0.683963 7 0.749721 8 0.809627 9 0.865007 10 0.908066 11 0.953274 12 1.001811 13 1.040129 14 1.068527 15 1.089111 16 1.111509 17 1.131483 18 1.140662 19 1.150016 20 1.165661 21 1.183386 22 1.192826 23 1.195432 24 1.197807 25 1.192478 26 1.18917 27 1.184804 28 1.186014 29 1.18052 30 1.175621 31 1.173977 32 1.167156 33 1.167753 34 1.160366 35 1.164442 36 1.164068 37 1.160785 38 1.158828 39 1.152384 40 1.147939 41 1.152341 42 1.150522 43 1.152558 44 1.148693 45 1.146056 46 1.140172 47 1.137528 48 1.134395 49 1.140486 50 1.143935 51 1.141691 52 1.135806 53 1.131023 54 1.134729 55 1.127148 56 1.116311 57 1.118131 58 1.120908 59 1.110603 60 1.10697 61 1.106646 62 1.106333 63 1.101386 64 1.093992 65 1.089728 66 1.09661 67 1.090914 68 1.082262 69 1.073595 70 1.060678 71 1.050044 72 1.042784 73 1.033 74 1.027333 75 1.023574 76 1.011857 77 0.995049 78 0.993749 79 0.986165 80 0.972587 81 0.956228 82 0.947088 83 0.934229 84 0.917799 85 0.900752 86 0.880984 87 0.86764 88 0.849807 89 0.830884 90 0.818058 91 0.794327 92 0.771457 93 0.747454 94 0.723963 95 0.699528 96 0.674911 97 0.646101 98 0.614763 99 0.5842 100 0.544365