## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT SkinN_FFPE_L07_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT SkinN_FFPE_L07_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: Thu May 28 22:48:56 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 45942870724 45032739903 65756 39259998575 3168395303 2185848909 418431360 0 0 0 9246847 160123555 850599 0.054595 0.945405 0.000001 0.87181 0.070358 0.048539 0.009292 0.942168 0.923503 0 0.784539 0.336661 0.548617 0.720445 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.299251 1 0.338456 2 0.397601 3 0.458332 4 0.511158 5 0.563309 6 0.611553 7 0.655712 8 0.701289 9 0.741215 10 0.767568 11 0.803865 12 0.841898 13 0.87585 14 0.915559 15 0.936173 16 0.958307 17 0.968926 18 0.974166 19 0.990889 20 1.005884 21 1.016801 22 1.024855 23 1.029005 24 1.040283 25 1.053941 26 1.061615 27 1.072392 28 1.086418 29 1.081394 30 1.087505 31 1.099134 32 1.112859 33 1.129489 34 1.121165 35 1.124769 36 1.130801 37 1.129913 38 1.145913 39 1.150585 40 1.16111 41 1.174704 42 1.183578 43 1.183431 44 1.187833 45 1.184326 46 1.167794 47 1.163746 48 1.15936 49 1.160874 50 1.160699 51 1.150252 52 1.149261 53 1.160083 54 1.171608 55 1.173309 56 1.176128 57 1.165467 58 1.157859 59 1.155744 60 1.169265 61 1.178428 62 1.180886 63 1.16208 64 1.15926 65 1.156085 66 1.152254 67 1.146562 68 1.152176 69 1.148859 70 1.141223 71 1.127678 72 1.123457 73 1.126258 74 1.127459 75 1.129522 76 1.137386 77 1.131031 78 1.116913 79 1.100602 80 1.080182 81 1.066008 82 1.048028 83 1.045951 84 1.042347 85 1.029018 86 1.012937 87 1.002399 88 0.985796 89 0.960728 90 0.925513 91 0.884165 92 0.842065 93 0.787953 94 0.755918 95 0.729478 96 0.686717 97 0.655973 98 0.611851 99 0.561876 100 0.51555