## 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_34.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_34_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 18:00:04 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 25341940272 25054976028 14190 21861905447 2028604637 1031288090 133163664 0 0 0 1425137 78274252 346594 0.017881 0.982119 0.000001 0.872557 0.080966 0.041161 0.005315 0.953524 0.942726 0 0.502471 0.562602 0.768224 0.845299 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.261707 1 0.300897 2 0.35916 3 0.425166 4 0.492654 5 0.558933 6 0.619893 7 0.677749 8 0.731976 9 0.785482 10 0.829885 11 0.87528 12 0.926396 13 0.969801 14 1.000244 15 1.027491 16 1.053655 17 1.071311 18 1.090375 19 1.106783 20 1.118418 21 1.133888 22 1.147107 23 1.156816 24 1.162339 25 1.165261 26 1.169312 27 1.176182 28 1.177455 29 1.174222 30 1.168763 31 1.165971 32 1.154302 33 1.152852 34 1.149655 35 1.147483 36 1.147824 37 1.139861 38 1.133335 39 1.136358 40 1.133537 41 1.133046 42 1.136645 43 1.139773 44 1.139809 45 1.150075 46 1.14987 47 1.150363 48 1.149162 49 1.155017 50 1.163374 51 1.16304 52 1.161283 53 1.160461 54 1.160489 55 1.162719 56 1.1591 57 1.158359 58 1.156594 59 1.148227 60 1.14388 61 1.146291 62 1.143785 63 1.138948 64 1.137567 65 1.137911 66 1.136907 67 1.131645 68 1.123189 69 1.114576 70 1.103744 71 1.097584 72 1.092943 73 1.083375 74 1.078661 75 1.07152 76 1.059123 77 1.039095 78 1.032137 79 1.024244 80 1.007515 81 0.98908 82 0.980429 83 0.965119 84 0.951028 85 0.944946 86 0.933106 87 0.914946 88 0.890241 89 0.871114 90 0.852536 91 0.827896 92 0.804257 93 0.774541 94 0.740543 95 0.706941 96 0.673707 97 0.638676 98 0.601605 99 0.561829 100 0.515635