## 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-49909d-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-49909d-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 20:03:05 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 63552510665 62659742376 23934 56156450351 4469851654 1707955375 325461062 0 0 0 9015964 207893493 974048 0.041566 0.958434 0 0.896213 0.071335 0.027258 0.005194 0.967548 0.953956 0 0.625369 0.491596 0.670735 0.836157 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.240963 1 0.279889 2 0.339062 3 0.404899 4 0.469973 5 0.537049 6 0.599468 7 0.65591 8 0.718893 9 0.769251 10 0.812797 11 0.865438 12 0.915626 13 0.963601 14 1.004801 15 1.041811 16 1.063012 17 1.08706 18 1.100171 19 1.109001 20 1.125648 21 1.142914 22 1.15787 23 1.176441 24 1.181958 25 1.1889 26 1.196444 27 1.199827 28 1.209954 29 1.211073 30 1.200612 31 1.201028 32 1.198487 33 1.199217 34 1.19404 35 1.19346 36 1.191305 37 1.188591 38 1.185634 39 1.182246 40 1.170959 41 1.167091 42 1.168371 43 1.165483 44 1.160806 45 1.161823 46 1.152188 47 1.150806 48 1.145956 49 1.14248 50 1.144439 51 1.138191 52 1.125708 53 1.127057 54 1.128683 55 1.125607 56 1.124522 57 1.119513 58 1.115313 59 1.113719 60 1.120202 61 1.128206 62 1.134865 63 1.126363 64 1.117987 65 1.120393 66 1.122451 67 1.121667 68 1.121241 69 1.119429 70 1.109124 71 1.09479 72 1.094092 73 1.091653 74 1.084648 75 1.077209 76 1.06589 77 1.054899 78 1.03905 79 1.023286 80 1.009209 81 0.990279 82 0.976659 83 0.957565 84 0.941588 85 0.929131 86 0.907613 87 0.89641 88 0.880227 89 0.861752 90 0.841021 91 0.818568 92 0.794807 93 0.76613 94 0.729122 95 0.695377 96 0.661376 97 0.623911 98 0.582575 99 0.545695 100 0.504826