## 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-7f9674-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-7f9674-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 20:17:01 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 73156460709 72395962925 4310 65817175964 4516910113 1855687794 206184744 0 0 0 10175169 238049520 1009628 0.040992 0.959008 0 0.909128 0.062392 0.025632 0.002848 0.971519 0.96142 0 0.540099 0.516435 0.712439 0.831833 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.294812 1 0.331943 2 0.385641 3 0.445593 4 0.499614 5 0.548486 6 0.608868 7 0.670015 8 0.722249 9 0.771131 10 0.821275 11 0.867467 12 0.918501 13 0.962448 14 0.999343 15 1.032737 16 1.054469 17 1.065997 18 1.078175 19 1.093712 20 1.114332 21 1.128017 22 1.14916 23 1.164382 24 1.170767 25 1.174908 26 1.178964 27 1.183959 28 1.189761 29 1.194093 30 1.195507 31 1.196643 32 1.190938 33 1.186057 34 1.177268 35 1.182614 36 1.182548 37 1.178738 38 1.180355 39 1.175859 40 1.169213 41 1.16431 42 1.166317 43 1.171591 44 1.169743 45 1.168366 46 1.158548 47 1.1607 48 1.155357 49 1.157816 50 1.159584 51 1.156691 52 1.154418 53 1.148532 54 1.141808 55 1.137428 56 1.133065 57 1.125618 58 1.117383 59 1.112465 60 1.104108 61 1.104402 62 1.109578 63 1.10931 64 1.108973 65 1.106666 66 1.102727 67 1.101439 68 1.100092 69 1.097736 70 1.093219 71 1.081772 72 1.077921 73 1.06943 74 1.061624 75 1.0579 76 1.053794 77 1.043954 78 1.03845 79 1.028666 80 1.016683 81 1.004262 82 0.992552 83 0.975906 84 0.958639 85 0.939896 86 0.918401 87 0.910753 88 0.89315 89 0.869419 90 0.840058 91 0.811846 92 0.782942 93 0.751176 94 0.727172 95 0.702643 96 0.672949 97 0.639881 98 0.604742 99 0.569433 100 0.536354