## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT aih-tih-sc-816ec7-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-816ec7-R1_A23YTGFLT4_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: Wed Jun 03 20:33:05 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 74653855755 73841441224 4424 66675998479 5087944951 1816026145 261467225 0 0 0 9993370 239902006 1174833 0.03999 0.96001 0 0.902962 0.068904 0.024594 0.003541 0.971865 0.961289 0 0.529583 0.573985 0.723481 0.898611 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.262531 1 0.305048 2 0.360451 3 0.429492 4 0.50086 5 0.569942 6 0.628123 7 0.688095 8 0.745031 9 0.796986 10 0.842651 11 0.885909 12 0.932684 13 0.97197 14 1.003408 15 1.031424 16 1.060189 17 1.081963 18 1.093951 19 1.109596 20 1.129077 21 1.144308 22 1.152967 23 1.165959 24 1.174323 25 1.174575 26 1.181405 27 1.187686 28 1.191242 29 1.187882 30 1.185232 31 1.18922 32 1.180114 33 1.182203 34 1.180658 35 1.184011 36 1.179898 37 1.17816 38 1.177604 39 1.177228 40 1.17237 41 1.170332 42 1.173826 43 1.172502 44 1.172563 45 1.185401 46 1.175466 47 1.172904 48 1.168956 49 1.166068 50 1.164947 51 1.156367 52 1.144841 53 1.139692 54 1.143075 55 1.143648 56 1.137332 57 1.131238 58 1.123521 59 1.117868 60 1.11426 61 1.114961 62 1.120412 63 1.114182 64 1.114326 65 1.116939 66 1.109985 67 1.103466 68 1.097736 69 1.096424 70 1.08907 71 1.080972 72 1.074284 73 1.066692 74 1.060403 75 1.055041 76 1.045729 77 1.034587 78 1.02546 79 1.01175 80 0.996769 81 0.982059 82 0.96835 83 0.95841 84 0.945914 85 0.93128 86 0.916648 87 0.90705 88 0.885555 89 0.862275 90 0.83717 91 0.817307 92 0.788046 93 0.759021 94 0.723001 95 0.686977 96 0.652082 97 0.615872 98 0.578536 99 0.543568 100 0.509431