## 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-f6bb6f-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-f6bb6f-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 20:58:57 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 75128524142 74295933928 4452 67608879278 4518755816 1963951791 204342591 0 0 0 5607162 244473617 1102430 0.022421 0.977579 0 0.909994 0.060821 0.026434 0.00275 0.970815 0.960057 0 0.518934 0.523164 0.740822 0.819322 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.278904 1 0.313679 2 0.369097 3 0.432495 4 0.490045 5 0.553627 6 0.616902 7 0.677186 8 0.738258 9 0.794421 10 0.839815 11 0.884039 12 0.928177 13 0.959239 14 0.994129 15 1.017274 16 1.047912 17 1.07236 18 1.082573 19 1.090757 20 1.099635 21 1.11294 22 1.125309 23 1.13914 24 1.140145 25 1.145438 26 1.147599 27 1.152469 28 1.160137 29 1.158457 30 1.163163 31 1.162598 32 1.160075 33 1.164944 34 1.160956 35 1.1699 36 1.180402 37 1.174771 38 1.168571 39 1.163186 40 1.163659 41 1.168393 42 1.170762 43 1.171547 44 1.170384 45 1.179117 46 1.181243 47 1.184167 48 1.185355 49 1.189144 50 1.191034 51 1.183374 52 1.175032 53 1.169002 54 1.169193 55 1.166564 56 1.166409 57 1.163809 58 1.158434 59 1.153954 60 1.150418 61 1.143765 62 1.145458 63 1.140517 64 1.139447 65 1.143049 66 1.136936 67 1.128581 68 1.11875 69 1.110832 70 1.093431 71 1.086043 72 1.075618 73 1.06535 74 1.055636 75 1.049524 76 1.037494 77 1.02347 78 1.022831 79 1.012065 80 0.996329 81 0.982872 82 0.972269 83 0.956152 84 0.938064 85 0.922735 86 0.899816 87 0.88871 88 0.871395 89 0.850924 90 0.831646 91 0.81225 92 0.78775 93 0.758325 94 0.726223 95 0.697504 96 0.665473 97 0.635611 98 0.60037 99 0.569943 100 0.529125