## 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_43.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_43_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 17:59:56 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 24694149901 24412351155 16310 21222103777 1973779328 1081462161 134989579 0 0 0 1222885 78302780 312945 0.015377 0.984623 0.000001 0.869318 0.080852 0.0443 0.00553 0.95017 0.939327 0 0.522528 0.564258 0.762056 0.829108 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.269319 1 0.308197 2 0.363423 3 0.425365 4 0.490858 5 0.557597 6 0.620837 7 0.681265 8 0.736772 9 0.788549 10 0.831336 11 0.879865 12 0.931384 13 0.971004 14 1.001613 15 1.026425 16 1.05155 17 1.069041 18 1.085592 19 1.098703 20 1.108496 21 1.124932 22 1.139148 23 1.148538 24 1.157325 25 1.159569 26 1.166198 27 1.172482 28 1.175786 29 1.172324 30 1.167334 31 1.164172 32 1.152756 33 1.152334 34 1.148221 35 1.149623 36 1.15101 37 1.143336 38 1.134994 39 1.133437 40 1.129659 41 1.128907 42 1.130786 43 1.135739 44 1.133731 45 1.141916 46 1.144323 47 1.14502 48 1.146576 49 1.155612 50 1.16281 51 1.161967 52 1.160376 53 1.159802 54 1.160196 55 1.161891 56 1.160321 57 1.158534 58 1.153925 59 1.148833 60 1.14745 61 1.148377 62 1.145776 63 1.140737 64 1.138175 65 1.139337 66 1.135856 67 1.129051 68 1.119398 69 1.11228 70 1.102602 71 1.096887 72 1.095149 73 1.087419 74 1.08169 75 1.075385 76 1.062756 77 1.043912 78 1.035701 79 1.022089 80 1.003984 81 0.984661 82 0.977087 83 0.964971 84 0.952782 85 0.947358 86 0.933679 87 0.916176 88 0.893252 89 0.873966 90 0.853489 91 0.829919 92 0.807688 93 0.779233 94 0.749882 95 0.717321 96 0.682456 97 0.646106 98 0.608334 99 0.56698 100 0.522478