## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT aih-tih-sc-966ec5-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-966ec5-R1_A23YTGFLT4_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 Jun 03 20:40:02 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 69561081395 68696493431 5004 61743265089 5050728777 1601688303 300806258 0 0 0 14431397 231623686 1099205 0.058651 0.941349 0 0.898783 0.073522 0.023315 0.004379 0.972306 0.960221 0 0.567736 0.510244 0.707958 0.847748 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.265952 1 0.306718 2 0.355329 3 0.412293 4 0.477955 5 0.547743 6 0.606546 7 0.660061 8 0.718372 9 0.766229 10 0.815473 11 0.870925 12 0.921705 13 0.961216 14 0.999364 15 1.026471 16 1.050816 17 1.072028 18 1.0826 19 1.102747 20 1.117711 21 1.129585 22 1.144387 23 1.156677 24 1.164934 25 1.167432 26 1.169139 27 1.165832 28 1.169101 29 1.165253 30 1.165234 31 1.168651 32 1.158337 33 1.160378 34 1.155523 35 1.149562 36 1.144001 37 1.141551 38 1.144345 39 1.144385 40 1.13869 41 1.142734 42 1.145387 43 1.142587 44 1.137385 45 1.147029 46 1.145821 47 1.144657 48 1.145299 49 1.153344 50 1.164798 51 1.160086 52 1.156977 53 1.155051 54 1.162712 55 1.165832 56 1.162623 57 1.159318 58 1.1512 59 1.143269 60 1.134573 61 1.13145 62 1.136961 63 1.134893 64 1.142611 65 1.145681 66 1.13594 67 1.13007 68 1.123973 69 1.114612 70 1.108373 71 1.101376 72 1.099197 73 1.091607 74 1.087144 75 1.078393 76 1.066653 77 1.052673 78 1.038639 79 1.035203 80 1.021963 81 1.007081 82 0.992044 83 0.969168 84 0.957102 85 0.941667 86 0.92103 87 0.908033 88 0.889571 89 0.872396 90 0.854065 91 0.835525 92 0.812609 93 0.784745 94 0.752667 95 0.715959 96 0.676383 97 0.640071 98 0.601246 99 0.561495 100 0.521413