## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT EndoN_FFPE_L06_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT EndoN_FFPE_L06_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 22:48:27 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 43603994671 42711556821 152969 36703929363 2833758302 2657936063 515780124 0 0 0 7884831 158712506 881017 0.047329 0.952671 0.000004 0.859344 0.066346 0.06223 0.012076 0.925691 0.906745 0 0.797436 0.357286 0.500213 0.764853 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.323361 1 0.36201 2 0.422895 3 0.490938 4 0.545219 5 0.595126 6 0.639388 7 0.679944 8 0.734295 9 0.783239 10 0.813191 11 0.848384 12 0.887267 13 0.92431 14 0.955161 15 0.974402 16 0.984963 17 0.989651 18 0.99699 19 1.010612 20 1.027679 21 1.040782 22 1.059228 23 1.071724 24 1.076242 25 1.085703 26 1.090046 27 1.103068 28 1.117557 29 1.11169 30 1.108896 31 1.123627 32 1.126086 33 1.133222 34 1.131499 35 1.137202 36 1.143515 37 1.14568 38 1.150316 39 1.153829 40 1.168269 41 1.183118 42 1.186095 43 1.182585 44 1.173882 45 1.165272 46 1.153492 47 1.146259 48 1.137578 49 1.132471 50 1.14613 51 1.152974 52 1.159848 53 1.170334 54 1.180335 55 1.176918 56 1.177678 57 1.172019 58 1.165339 59 1.171249 60 1.19037 61 1.200175 62 1.201951 63 1.181509 64 1.178927 65 1.172887 66 1.160872 67 1.1471 68 1.132826 69 1.128161 70 1.114158 71 1.109015 72 1.105859 73 1.104962 74 1.111066 75 1.111534 76 1.120645 77 1.123728 78 1.112205 79 1.081231 80 1.058932 81 1.032782 82 1.009395 83 0.991601 84 0.983096 85 0.964214 86 0.948138 87 0.938337 88 0.923366 89 0.894976 90 0.861743 91 0.829266 92 0.79795 93 0.767803 94 0.736213 95 0.700676 96 0.656386 97 0.613516 98 0.569101 99 0.518291 100 0.471735