## 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_00081_23KKJ7LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00081_23KKJ7LT4_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: Thu Mar 05 20:23:26 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 24815415357 24387668904 49778 17587983638 2427919189 3974686466 397029833 0 0 0 952559 67872710 273617 0.01384 0.98616 0.000002 0.721183 0.099555 0.162979 0.01628 0.820739 0.806591 0 0.551339 0.51182 0.703843 0.88879 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.304798 1 0.3411 2 0.394762 3 0.456521 4 0.513546 5 0.559771 6 0.623851 7 0.683491 8 0.740629 9 0.790583 10 0.83901 11 0.883643 12 0.93227 13 0.969106 14 0.998371 15 1.022847 16 1.049187 17 1.071935 18 1.086906 19 1.096263 20 1.112679 21 1.128722 22 1.145539 23 1.160024 24 1.169291 25 1.169211 26 1.166774 27 1.165375 28 1.166024 29 1.162274 30 1.165309 31 1.164297 32 1.164533 33 1.168956 34 1.172797 35 1.18208 36 1.178642 37 1.172785 38 1.17156 39 1.17126 40 1.166365 41 1.163888 42 1.172531 43 1.18302 44 1.181512 45 1.185479 46 1.186414 47 1.184016 48 1.186866 49 1.192894 50 1.180723 51 1.175237 52 1.166349 53 1.157883 54 1.153845 55 1.147609 56 1.142768 57 1.137989 58 1.125792 59 1.112436 60 1.104122 61 1.09871 62 1.096523 63 1.093353 64 1.091615 65 1.087416 66 1.083708 67 1.077726 68 1.07332 69 1.069273 70 1.065578 71 1.058625 72 1.058775 73 1.050801 74 1.043847 75 1.040068 76 1.037193 77 1.032892 78 1.030326 79 1.017761 80 1.009752 81 0.994047 82 0.984816 83 0.971548 84 0.962891 85 0.951827 86 0.932666 87 0.913754 88 0.891586 89 0.871389 90 0.850871 91 0.823645 92 0.800697 93 0.770707 94 0.737874 95 0.710822 96 0.682531 97 0.651458 98 0.615734 99 0.580081 100 0.53931