## 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_00473_23KMKGLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00473_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 23:37:28 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 24947748593 24632701822 14024 22111785523 1707228300 721342493 92331482 0 0 0 2880331 79352055 289801 0.035027 0.964973 0.000001 0.89766 0.069307 0.029284 0.003748 0.966967 0.954756 0 0.540307 0.570027 0.708221 0.903654 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.300895 1 0.343846 2 0.406853 3 0.483172 4 0.548708 5 0.60258 6 0.66604 7 0.721468 8 0.776722 9 0.824301 10 0.874286 11 0.926 12 0.968085 13 1.004774 14 1.029576 15 1.04961 16 1.070191 17 1.094121 18 1.107001 19 1.115558 20 1.131576 21 1.150458 22 1.165389 23 1.176964 24 1.181642 25 1.186788 26 1.192545 27 1.196044 28 1.199995 29 1.202807 30 1.204986 31 1.202521 32 1.204423 33 1.200682 34 1.206571 35 1.204789 36 1.195892 37 1.184554 38 1.181288 39 1.188629 40 1.194892 41 1.193453 42 1.19398 43 1.199457 44 1.192913 45 1.188159 46 1.17682 47 1.169567 48 1.159178 49 1.168047 50 1.16667 51 1.16417 52 1.165097 53 1.153606 54 1.152025 55 1.145259 56 1.138281 57 1.140349 58 1.131387 59 1.112674 60 1.108557 61 1.10966 62 1.113248 63 1.113187 64 1.108825 65 1.107467 66 1.092652 67 1.080527 68 1.067929 69 1.064272 70 1.058531 71 1.050045 72 1.045575 73 1.034342 74 1.022641 75 1.00995 76 0.998913 77 0.989505 78 0.986942 79 0.984517 80 0.963224 81 0.946398 82 0.933161 83 0.917794 84 0.904008 85 0.896018 86 0.879495 87 0.863813 88 0.84578 89 0.825839 90 0.808572 91 0.784626 92 0.755941 93 0.726554 94 0.712976 95 0.684029 96 0.642878 97 0.615823 98 0.582644 99 0.546587 100 0.509979