## 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_25.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_25_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 17:59:38 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 25332132072 25047683973 13054 22023797379 2008654031 886749053 128470456 0 0 0 1573536 78452494 335961 0.019663 0.980337 0.000001 0.879275 0.080193 0.035402 0.005129 0.959468 0.948694 0 0.515606 0.579707 0.736452 0.893054 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.268195 1 0.308258 2 0.369509 3 0.437091 4 0.506341 5 0.576077 6 0.639995 7 0.701337 8 0.756246 9 0.811048 10 0.856592 11 0.901998 12 0.952308 13 1.000443 14 1.035152 15 1.063584 16 1.089769 17 1.105091 18 1.117663 19 1.134243 20 1.146631 21 1.164539 22 1.17382 23 1.183231 24 1.18903 25 1.19087 26 1.197013 27 1.203363 28 1.203417 29 1.195244 30 1.187651 31 1.181245 32 1.168309 33 1.164037 34 1.157904 35 1.155244 36 1.152812 37 1.146509 38 1.139408 39 1.140253 40 1.137003 41 1.137353 42 1.139554 43 1.143388 44 1.141085 45 1.150171 46 1.150364 47 1.149119 48 1.146649 49 1.152971 50 1.159797 51 1.161145 52 1.161374 53 1.159876 54 1.160274 55 1.159598 56 1.153469 57 1.150888 58 1.147456 59 1.138487 60 1.132618 61 1.134817 62 1.134656 63 1.126631 64 1.119491 65 1.116918 66 1.113887 67 1.11028 68 1.101917 69 1.091112 70 1.084557 71 1.077253 72 1.071106 73 1.060847 74 1.052832 75 1.04698 76 1.035447 77 1.015339 78 1.00811 79 1.001618 80 0.984141 81 0.967282 82 0.959896 83 0.942822 84 0.929565 85 0.922412 86 0.910157 87 0.891761 88 0.868773 89 0.84713 90 0.830411 91 0.807436 92 0.785965 93 0.758512 94 0.723965 95 0.690093 96 0.657561 97 0.62393 98 0.589082 99 0.551182 100 0.507316