## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT tih_rna_sample_00157_23KMKGLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00157_23KMKGLT4_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 Mar 04 23:42:18 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 24329509470 23973944513 12408 21229473299 1662006826 976121667 106330313 0 0 0 1686947 78346549 256119 0.021078 0.978922 0.000001 0.885523 0.069326 0.040716 0.004435 0.954848 0.940894 0 0.550463 0.559691 0.745135 0.860623 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.263506 1 0.301501 2 0.354994 3 0.421587 4 0.492442 5 0.566526 6 0.63179 7 0.688762 8 0.743725 9 0.790617 10 0.837401 11 0.885124 12 0.933997 13 0.970848 14 1.003096 15 1.028615 16 1.055937 17 1.07914 18 1.096268 19 1.11388 20 1.123401 21 1.142373 22 1.155509 23 1.173259 24 1.180826 25 1.182731 26 1.185907 27 1.185227 28 1.186062 29 1.185272 30 1.183864 31 1.179601 32 1.174005 33 1.167035 34 1.162693 35 1.159487 36 1.155352 37 1.147494 38 1.139765 39 1.135528 40 1.134705 41 1.132915 42 1.131154 43 1.132647 44 1.135005 45 1.142201 46 1.136192 47 1.131101 48 1.133333 49 1.139868 50 1.140186 51 1.13712 52 1.131207 53 1.134794 54 1.142605 55 1.142479 56 1.1433 57 1.144409 58 1.140142 59 1.130013 60 1.123981 61 1.12701 62 1.131787 63 1.127938 64 1.128382 65 1.1288 66 1.122539 67 1.11265 68 1.112225 69 1.10885 70 1.095256 71 1.091058 72 1.088043 73 1.081886 74 1.081182 75 1.081777 76 1.070858 77 1.055108 78 1.050529 79 1.039355 80 1.022977 81 1.003718 82 0.992182 83 0.973198 84 0.962606 85 0.95642 86 0.936735 87 0.918721 88 0.896805 89 0.880017 90 0.85853 91 0.830168 92 0.803202 93 0.77212 94 0.736471 95 0.69879 96 0.666964 97 0.63326 98 0.592662 99 0.550609 100 0.504993