## 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-67e6e5-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-67e6e5-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 20:40:58 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 71896378629 70975117677 6730 62467229300 5903425632 2218573299 385882716 0 0 0 12723297 231371591 1235729 0.052124 0.947876 0 0.880129 0.083176 0.031258 0.005437 0.963305 0.950961 0 0.632295 0.586933 0.583093 1.088204 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.359668 1 0.405309 2 0.46585 3 0.531327 4 0.607924 5 0.685168 6 0.746879 7 0.808543 8 0.867217 9 0.919065 10 0.97792 11 1.036237 12 1.086102 13 1.122186 14 1.147918 15 1.161979 16 1.171516 17 1.183767 18 1.195999 19 1.20205 20 1.20755 21 1.218231 22 1.226597 23 1.231741 24 1.2348 25 1.239434 26 1.242191 27 1.239599 28 1.238996 29 1.238086 30 1.231887 31 1.221047 32 1.209037 33 1.203377 34 1.196268 35 1.190684 36 1.194043 37 1.187207 38 1.165727 39 1.146475 40 1.137062 41 1.127406 42 1.123528 43 1.123581 44 1.116507 45 1.127196 46 1.128563 47 1.133244 48 1.128664 49 1.133413 50 1.133975 51 1.135684 52 1.138661 53 1.135322 54 1.131185 55 1.122625 56 1.115448 57 1.107352 58 1.096966 59 1.085415 60 1.086698 61 1.095189 62 1.097797 63 1.079876 64 1.071759 65 1.074567 66 1.075661 67 1.067275 68 1.05544 69 1.040142 70 1.018544 71 0.999186 72 0.99174 73 0.984284 74 0.973411 75 0.961636 76 0.952193 77 0.943196 78 0.936473 79 0.929424 80 0.916487 81 0.904336 82 0.896855 83 0.884845 84 0.868267 85 0.848035 86 0.824987 87 0.810026 88 0.796553 89 0.779781 90 0.762931 91 0.749567 92 0.729911 93 0.702771 94 0.67276 95 0.648962 96 0.624785 97 0.599938 98 0.568548 99 0.538618 100 0.502488