## 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_00566_23LGNLLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00566_23LGNLLT4_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: Sat May 16 10:04:40 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 78008837624 77112567243 56233 66602671544 5599013212 4277797477 633028777 0 0 0 9367397 218343271 829430 0.041137 0.958863 0.000001 0.863707 0.072608 0.055475 0.008209 0.936315 0.925558 0 0.516175 0.549897 0.687429 0.960158 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.274879 1 0.317944 2 0.380882 3 0.449901 4 0.518933 5 0.584991 6 0.645651 7 0.701825 8 0.759111 9 0.809915 10 0.859375 11 0.910438 12 0.960163 13 0.995757 14 1.018861 15 1.048804 16 1.073275 17 1.103472 18 1.11485 19 1.123702 20 1.138577 21 1.153522 22 1.171801 23 1.190785 24 1.196837 25 1.197604 26 1.193883 27 1.19155 28 1.185132 29 1.183531 30 1.184369 31 1.185427 32 1.183358 33 1.184658 34 1.177249 35 1.180479 36 1.179715 37 1.180052 38 1.179435 39 1.170791 40 1.164296 41 1.164612 42 1.167769 43 1.168083 44 1.165143 45 1.168146 46 1.157989 47 1.153324 48 1.153337 49 1.149051 50 1.150218 51 1.148851 52 1.140362 53 1.137829 54 1.146194 55 1.147111 56 1.146606 57 1.14229 58 1.139844 59 1.12669 60 1.120791 61 1.123991 62 1.134628 63 1.127727 64 1.125365 65 1.128076 66 1.12331 67 1.119534 68 1.111479 69 1.103372 70 1.093164 71 1.08222 72 1.075224 73 1.068209 74 1.054962 75 1.047693 76 1.036963 77 1.018087 78 1.012418 79 1.011995 80 0.999557 81 0.98066 82 0.966736 83 0.941429 84 0.921308 85 0.904139 86 0.885505 87 0.865865 88 0.845451 89 0.82214 90 0.799481 91 0.775331 92 0.749805 93 0.72272 94 0.696435 95 0.67105 96 0.644769 97 0.61231 98 0.577797 99 0.544797 100 0.511438