## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT ColoN_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT ColoN_FFPE_L01_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: Sat May 16 08:39:06 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 2783768389 2693443349 168979 2139939424 198065456 308340603 46928887 0 0 0 869545 9725511 69054 0.082071 0.917929 0.000063 0.7945 0.073536 0.114478 0.017423 0.868036 0.83987 0 0.793186 0.337775 0.555742 0.459336 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.275834 1 0.310552 2 0.366162 3 0.428361 4 0.483578 5 0.542882 6 0.606477 7 0.664344 8 0.723212 9 0.781532 10 0.820251 11 0.854195 12 0.868928 13 0.902148 14 0.934569 15 0.951856 16 0.969989 17 0.972466 18 0.984952 19 1.009534 20 1.027626 21 1.040007 22 1.047501 23 1.061556 24 1.064295 25 1.066741 26 1.068409 27 1.071022 28 1.087411 29 1.088725 30 1.08986 31 1.097647 32 1.112262 33 1.125827 34 1.13043 35 1.147445 36 1.161704 37 1.170251 38 1.177449 39 1.178269 40 1.171206 41 1.184817 42 1.175046 43 1.166687 44 1.166992 45 1.164274 46 1.151145 47 1.143929 48 1.147239 49 1.150778 50 1.156885 51 1.161559 52 1.156202 53 1.161001 54 1.163865 55 1.154802 56 1.158336 57 1.161876 58 1.155819 59 1.149291 60 1.151413 61 1.151595 62 1.156639 63 1.14713 64 1.154952 65 1.163445 66 1.156594 67 1.147062 68 1.140666 69 1.129028 70 1.122471 71 1.101003 72 1.0916 73 1.088872 74 1.09658 75 1.094714 76 1.102324 77 1.102045 78 1.084063 79 1.062124 80 1.052804 81 1.040057 82 1.021638 83 1.012254 84 1.004955 85 0.992962 86 0.994735 87 0.986397 88 0.978781 89 0.977544 90 0.953708 91 0.932222 92 0.896895 93 0.842008 94 0.80188 95 0.759044 96 0.716764 97 0.67132 98 0.617884 99 0.565433 100 0.514693