## 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_00149_23KMKGLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00149_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 23:36:17 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 23682363695 23378663035 12412 20076368842 1710041468 1437739383 154500930 0 0 0 2641380 76579857 252195 0.033342 0.966658 0.000001 0.858748 0.073145 0.061498 0.006609 0.931893 0.919942 0 0.559965 0.529428 0.745194 0.804245 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.286187 1 0.320799 2 0.373675 3 0.437828 4 0.494737 5 0.553544 6 0.608698 7 0.663658 8 0.712901 9 0.762287 10 0.806329 11 0.854648 12 0.897963 13 0.931887 14 0.966944 15 0.995567 16 1.018037 17 1.036338 18 1.048336 19 1.058993 20 1.079425 21 1.098201 22 1.115744 23 1.134025 24 1.138926 25 1.139076 26 1.14618 27 1.157842 28 1.166383 29 1.16688 30 1.165929 31 1.162399 32 1.164584 33 1.169974 34 1.17193 35 1.177378 36 1.180219 37 1.179964 38 1.1819 39 1.180849 40 1.178171 41 1.179198 42 1.179921 43 1.178468 44 1.176861 45 1.182176 46 1.178227 47 1.174946 48 1.173654 49 1.17487 50 1.176452 51 1.167624 52 1.152262 53 1.141315 54 1.145247 55 1.144334 56 1.145445 57 1.141308 58 1.137447 59 1.129296 60 1.12739 61 1.133161 62 1.128555 63 1.122622 64 1.123584 65 1.125425 66 1.121206 67 1.110958 68 1.106768 69 1.106679 70 1.096536 71 1.087641 72 1.080168 73 1.06777 74 1.055699 75 1.047148 76 1.046127 77 1.041195 78 1.037107 79 1.027686 80 1.022066 81 1.010169 82 0.996981 83 0.981049 84 0.975036 85 0.963825 86 0.942636 87 0.928342 88 0.910977 89 0.896599 90 0.871054 91 0.842352 92 0.81677 93 0.78508 94 0.752685 95 0.722416 96 0.691215 97 0.656895 98 0.6205 99 0.585951 100 0.543581