## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2_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 Mar 04 00:18:10 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 15320795090 14685801339 69925 12501011652 1204561539 782432581 197725642 0 0 0 5118262 57161443 336563 0.082182 0.917818 0.000005 0.851231 0.082022 0.053278 0.013464 0.933253 0.894573 0 0.891572 0.354418 0.446786 0.690367 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.269641 1 0.309783 2 0.379051 3 0.462351 4 0.54795 5 0.6305 6 0.708902 7 0.785893 8 0.853722 9 0.902689 10 0.936436 11 0.966074 12 1.002096 13 1.04469 14 1.080221 15 1.106179 16 1.121459 17 1.136319 18 1.12406 19 1.110685 20 1.116293 21 1.117862 22 1.124997 23 1.13499 24 1.145638 25 1.13868 26 1.128286 27 1.136435 28 1.154424 29 1.151193 30 1.151832 31 1.162451 32 1.146027 33 1.152544 34 1.144087 35 1.129855 36 1.130885 37 1.129833 38 1.127093 39 1.125206 40 1.128391 41 1.147963 42 1.157169 43 1.158504 44 1.164396 45 1.175636 46 1.166541 47 1.15196 48 1.1383 49 1.131302 50 1.136128 51 1.130118 52 1.122816 53 1.1197 54 1.118508 55 1.118432 56 1.105688 57 1.099111 58 1.096434 59 1.074729 60 1.075701 61 1.092983 62 1.110452 63 1.105363 64 1.103853 65 1.102895 66 1.11037 67 1.088842 68 1.084297 69 1.082284 70 1.068479 71 1.056255 72 1.053898 73 1.056303 74 1.055556 75 1.06466 76 1.076837 77 1.063123 78 1.046082 79 1.041917 80 1.037411 81 1.021248 82 0.998989 83 0.99092 84 0.978944 85 0.965015 86 0.948477 87 0.928654 88 0.90646 89 0.873788 90 0.854858 91 0.825775 92 0.77814 93 0.743217 94 0.710428 95 0.675106 96 0.635344 97 0.598447 98 0.561202 99 0.520815 100 0.474394