## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT U118MG_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam --OUTPUT U118MG_FFPE_RNA_0001_B23LG7FLT4_3_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 21:28:54 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 75950584146 75034671496 40858 67026170969 4682201275 2854676242 471582152 0 0 0 6044080 235298213 1430493 0.025044 0.974956 0.000001 0.893269 0.062401 0.038045 0.006285 0.95567 0.944145 0 0.503627 0.619251 0.731669 0.973209 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.320534 1 0.363183 2 0.418348 3 0.487379 4 0.548037 5 0.607746 6 0.674132 7 0.737447 8 0.793459 9 0.852395 10 0.899537 11 0.948746 12 0.995101 13 1.033465 14 1.065958 15 1.100358 16 1.126982 17 1.140089 18 1.146208 19 1.150115 20 1.167129 21 1.186693 22 1.195265 23 1.208936 24 1.211672 25 1.213698 26 1.213906 27 1.209211 28 1.203974 29 1.193432 30 1.189854 31 1.185067 32 1.179542 33 1.181192 34 1.174609 35 1.176198 36 1.173534 37 1.166942 38 1.168696 39 1.16762 40 1.166423 41 1.166047 42 1.162518 43 1.162185 44 1.156251 45 1.156429 46 1.155388 47 1.153598 48 1.151338 49 1.152239 50 1.15122 51 1.155977 52 1.152356 53 1.149902 54 1.150534 55 1.151786 56 1.145931 57 1.141463 58 1.133873 59 1.118735 60 1.10753 61 1.10342 62 1.105404 63 1.103136 64 1.092278 65 1.084913 66 1.083089 67 1.074832 68 1.067629 69 1.061441 70 1.052733 71 1.041305 72 1.036699 73 1.022968 74 1.008703 75 1.001213 76 0.993402 77 0.976537 78 0.96793 79 0.959159 80 0.944568 81 0.930979 82 0.920624 83 0.901878 84 0.891242 85 0.881854 86 0.867644 87 0.852884 88 0.837132 89 0.820898 90 0.806532 91 0.781118 92 0.756467 93 0.731579 94 0.703027 95 0.679956 96 0.658294 97 0.632318 98 0.608365 99 0.581036 100 0.549536