## 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-f7ac14-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-f7ac14-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 22:40:35 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 63604727372 62699941302 9764 56893877417 3946183753 1590945080 268925288 0 0 0 7731116 229053385 926755 0.03265 0.96735 0 0.907399 0.062938 0.025374 0.004289 0.970337 0.956534 0 0.618465 0.515601 0.653259 0.854555 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.291511 1 0.327941 2 0.388966 3 0.456461 4 0.525299 5 0.595397 6 0.656928 7 0.712022 8 0.768501 9 0.819857 10 0.868689 11 0.920686 12 0.964632 13 0.998905 14 1.029551 15 1.042784 16 1.066408 17 1.086728 18 1.086825 19 1.104282 20 1.127815 21 1.143202 22 1.155931 23 1.16374 24 1.171073 25 1.168492 26 1.165683 27 1.176086 28 1.181437 29 1.171127 30 1.153258 31 1.150869 32 1.150713 33 1.159666 34 1.155748 35 1.152197 36 1.145156 37 1.13787 38 1.139044 39 1.143522 40 1.146745 41 1.154278 42 1.161947 43 1.16762 44 1.17021 45 1.180014 46 1.179996 47 1.18194 48 1.169998 49 1.167733 50 1.149331 51 1.140987 52 1.132572 53 1.128349 54 1.136616 55 1.136003 56 1.127993 57 1.127379 58 1.124979 59 1.12243 60 1.128278 61 1.139674 62 1.149835 63 1.138239 64 1.141289 65 1.140429 66 1.131014 67 1.121783 68 1.109747 69 1.104162 70 1.092967 71 1.07527 72 1.073257 73 1.06047 74 1.050987 75 1.046379 76 1.038571 77 1.026724 78 1.012528 79 0.992558 80 0.985339 81 0.979244 82 0.964003 83 0.953814 84 0.939441 85 0.926825 86 0.907703 87 0.899357 88 0.883198 89 0.861293 90 0.837012 91 0.822075 92 0.79367 93 0.759031 94 0.723536 95 0.691064 96 0.658303 97 0.62676 98 0.587782 99 0.548584 100 0.507757