## 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-ecc0bc-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-ecc0bc-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 21:12:57 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 55325525526 54607181650 8730 49136816555 3560247216 1699927182 210181967 0 0 0 8590919 193425434 833466 0.042526 0.957474 0 0.899823 0.065197 0.03113 0.003849 0.965021 0.952491 0 0.589605 0.488249 0.727551 0.771071 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.322329 1 0.353183 2 0.404819 3 0.464967 4 0.50815 5 0.5509 6 0.611968 7 0.666913 8 0.716715 9 0.756349 10 0.790288 11 0.838707 12 0.881234 13 0.918334 14 0.952634 15 0.975669 16 0.992144 17 1.005494 18 1.012942 19 1.025458 20 1.038152 21 1.04838 22 1.066509 23 1.086447 24 1.096105 25 1.102609 26 1.109594 27 1.119488 28 1.133543 29 1.13585 30 1.138007 31 1.142032 32 1.140641 33 1.152093 34 1.146404 35 1.156668 36 1.161619 37 1.161252 38 1.163183 39 1.165138 40 1.163033 41 1.159143 42 1.169029 43 1.181252 44 1.18782 45 1.202305 46 1.201605 47 1.197221 48 1.191987 49 1.188407 50 1.181267 51 1.175844 52 1.170218 53 1.166517 54 1.165619 55 1.167194 56 1.159585 57 1.149434 58 1.141323 59 1.138102 60 1.141054 61 1.145654 62 1.151412 63 1.140013 64 1.136802 65 1.136368 66 1.125378 67 1.121841 68 1.123247 69 1.120013 70 1.10731 71 1.094921 72 1.090797 73 1.087388 74 1.084106 75 1.07372 76 1.066036 77 1.055168 78 1.04227 79 1.034371 80 1.024555 81 1.013316 82 0.999902 83 0.988381 84 0.977017 85 0.966142 86 0.94717 87 0.936177 88 0.920368 89 0.905534 90 0.887068 91 0.866129 92 0.836026 93 0.803076 94 0.771154 95 0.742231 96 0.71023 97 0.675701 98 0.634011 99 0.589284 100 0.544919