## 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-885658-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-885658-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 20:37:55 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 67599429522 66807350786 9559 59107033368 5106511738 2288389450 305406671 0 0 0 9339740 214534327 1002266 0.041719 0.958281 0 0.884738 0.076436 0.034254 0.004571 0.961175 0.949913 0 0.565581 0.504819 0.741851 0.801959 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.316057 1 0.353074 2 0.407242 3 0.464167 4 0.517464 5 0.5699 6 0.618617 7 0.664447 8 0.710465 9 0.749002 10 0.786313 11 0.831662 12 0.87415 13 0.907722 14 0.935274 15 0.954949 16 0.979625 17 0.998561 18 1.014598 19 1.028288 20 1.04697 21 1.068228 22 1.087094 23 1.105994 24 1.118851 25 1.127465 26 1.128386 27 1.132111 28 1.138663 29 1.139478 30 1.136629 31 1.143445 32 1.143767 33 1.146058 34 1.137315 35 1.137032 36 1.126504 37 1.119583 38 1.120654 39 1.116429 40 1.11545 41 1.113405 42 1.117236 43 1.121288 44 1.12398 45 1.134342 46 1.133934 47 1.13984 48 1.138716 49 1.137339 50 1.141116 51 1.137137 52 1.138543 53 1.14113 54 1.145496 55 1.145401 56 1.146779 57 1.142619 58 1.138301 59 1.138371 60 1.142144 61 1.146778 62 1.151551 63 1.143337 64 1.147603 65 1.157647 66 1.160282 67 1.158512 68 1.156501 69 1.152764 70 1.139647 71 1.132195 72 1.131126 73 1.127004 74 1.118475 75 1.113274 76 1.104483 77 1.092466 78 1.081606 79 1.078629 80 1.067349 81 1.057358 82 1.04175 83 1.026205 84 1.012855 85 0.994629 86 0.969465 87 0.952252 88 0.935625 89 0.919898 90 0.899406 91 0.880024 92 0.848686 93 0.811894 94 0.775367 95 0.741067 96 0.704862 97 0.665993 98 0.626025 99 0.585961 100 0.54175