## 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_1.Aligned.sortedByCoord.out.bam --OUTPUT U118MG_FFPE_RNA_0001_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: Fri Feb 27 07:06:52 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 25468215089 25137248648 13362 22459047204 1584715497 932542432 160930153 0 0 0 3940646 76438008 491787 0.049026 0.950974 0.000001 0.893457 0.063043 0.037098 0.006402 0.956499 0.944069 0 0.503006 0.619999 0.735341 0.978561 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.320064 1 0.364362 2 0.418753 3 0.486488 4 0.545792 5 0.603364 6 0.668934 7 0.733207 8 0.788948 9 0.848883 10 0.897327 11 0.94783 12 0.992961 13 1.02837 14 1.060659 15 1.098036 16 1.12741 17 1.142807 18 1.151863 19 1.154782 20 1.17287 21 1.19165 22 1.199085 23 1.213012 24 1.214932 25 1.213766 26 1.214812 27 1.211454 28 1.207424 29 1.198527 30 1.195202 31 1.193091 32 1.186796 33 1.189243 34 1.183388 35 1.185713 36 1.18202 37 1.175482 38 1.174517 39 1.171804 40 1.172635 41 1.171844 42 1.170939 43 1.169409 44 1.163846 45 1.162902 46 1.1606 47 1.159324 48 1.157444 49 1.159347 50 1.156937 51 1.159066 52 1.153748 53 1.152325 54 1.153984 55 1.15475 56 1.14864 57 1.143724 58 1.134615 59 1.123164 60 1.111655 61 1.106828 62 1.104369 63 1.100493 64 1.090729 65 1.082377 66 1.076315 67 1.064905 68 1.058461 69 1.052581 70 1.043785 71 1.033972 72 1.031721 73 1.01844 74 1.002814 75 0.993554 76 0.984146 77 0.961213 78 0.953011 79 0.945535 80 0.933701 81 0.920651 82 0.910449 83 0.893383 84 0.884458 85 0.876095 86 0.860393 87 0.843527 88 0.828438 89 0.81216 90 0.800168 91 0.77951 92 0.757135 93 0.734876 94 0.711716 95 0.688382 96 0.666536 97 0.638597 98 0.613997 99 0.586454 100 0.551591