## 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-184b05-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-184b05-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 20:45:59 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 76005487780 75029922347 4840 67389831478 5327724630 2043832285 268529114 0 0 0 9607984 238559248 1198580 0.038716 0.961284 0 0.898173 0.071008 0.02724 0.003579 0.969181 0.956741 0 0.553963 0.569851 0.671907 0.928366 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.288842 1 0.339492 2 0.401422 3 0.477284 4 0.556317 5 0.627297 6 0.694387 7 0.759028 8 0.817826 9 0.865644 10 0.910708 11 0.951383 12 0.982483 13 1.018239 14 1.049209 15 1.072638 16 1.095187 17 1.108501 18 1.124839 19 1.138512 20 1.157598 21 1.167503 22 1.174084 23 1.183761 24 1.184419 25 1.181655 26 1.179102 27 1.171941 28 1.170737 29 1.173729 30 1.175703 31 1.174632 32 1.170261 33 1.172295 34 1.16428 35 1.166566 36 1.15864 37 1.149588 38 1.154128 39 1.152352 40 1.148241 41 1.143754 42 1.1494 43 1.153214 44 1.151351 45 1.161243 46 1.158685 47 1.16084 48 1.153709 49 1.14735 50 1.136313 51 1.13049 52 1.122339 53 1.122625 54 1.123998 55 1.127422 56 1.125407 57 1.122498 58 1.116371 59 1.108837 60 1.104128 61 1.108179 62 1.109547 63 1.101766 64 1.103993 65 1.105938 66 1.106568 67 1.103202 68 1.103143 69 1.093403 70 1.080456 71 1.068935 72 1.067267 73 1.064075 74 1.056775 75 1.048387 76 1.040086 77 1.022264 78 1.00819 79 0.995775 80 0.979625 81 0.965465 82 0.951014 83 0.935835 84 0.922201 85 0.904599 86 0.883092 87 0.871747 88 0.852838 89 0.837934 90 0.817473 91 0.801803 92 0.773182 93 0.740574 94 0.707716 95 0.67765 96 0.648126 97 0.62119 98 0.586949 99 0.553521 100 0.516654