## 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_26.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_26_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 17:59:42 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 25658779609 25367974575 8218 22083552196 2075741935 1071060764 137611462 0 0 0 1581154 78017200 340664 0.019864 0.980136 0 0.870529 0.081825 0.042221 0.005425 0.952354 0.941561 0 0.495582 0.574534 0.765254 0.828145 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.269685 1 0.307878 2 0.36513 3 0.432268 4 0.499606 5 0.564646 6 0.625484 7 0.684477 8 0.738187 9 0.791588 10 0.835825 11 0.882216 12 0.929851 13 0.969638 14 0.999996 15 1.025359 16 1.051313 17 1.070409 18 1.090476 19 1.107511 20 1.12154 21 1.136533 22 1.147759 23 1.155272 24 1.164312 25 1.167912 26 1.172371 27 1.179012 28 1.179144 29 1.176395 30 1.170442 31 1.167344 32 1.154604 33 1.151984 34 1.146909 35 1.145333 36 1.148648 37 1.141255 38 1.133796 39 1.134115 40 1.128768 41 1.128064 42 1.134556 43 1.141225 44 1.141016 45 1.153463 46 1.153174 47 1.153986 48 1.15106 49 1.157233 50 1.164971 51 1.16555 52 1.162899 53 1.16151 54 1.161711 55 1.163435 56 1.162168 57 1.161062 58 1.159936 59 1.152973 60 1.148228 61 1.14908 62 1.144702 63 1.138417 64 1.135567 65 1.136026 66 1.135096 67 1.130962 68 1.122327 69 1.114016 70 1.106024 71 1.098615 72 1.093175 73 1.082564 74 1.077297 75 1.06763 76 1.05414 77 1.035001 78 1.02805 79 1.017826 80 0.998528 81 0.98004 82 0.971535 83 0.958686 84 0.946572 85 0.93947 86 0.925037 87 0.908561 88 0.884966 89 0.865546 90 0.845207 91 0.821184 92 0.799073 93 0.770226 94 0.740796 95 0.708181 96 0.672962 97 0.636675 98 0.600005 99 0.5607 100 0.515015