## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_19.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_19_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: Mon Mar 09 17:59:38 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 25227920886 24928632471 12376 21638908959 2057119920 1089190371 143400845 0 0 0 2005620 77518873 320337 0.02522 0.97478 0 0.868034 0.08252 0.043692 0.005752 0.950555 0.939278 0 0.514687 0.578613 0.765575 0.843871 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.277899 1 0.317093 2 0.374938 3 0.437986 4 0.504585 5 0.571985 6 0.636876 7 0.69801 8 0.751963 9 0.803094 10 0.847264 11 0.892873 12 0.941823 13 0.980202 14 1.008591 15 1.034616 16 1.060427 17 1.078036 18 1.09056 19 1.105073 20 1.119092 21 1.135339 22 1.145181 23 1.154423 24 1.163959 25 1.167119 26 1.172614 27 1.17849 28 1.180739 29 1.179948 30 1.176608 31 1.175061 32 1.164742 33 1.162844 34 1.156877 35 1.156409 36 1.157404 37 1.149125 38 1.140671 39 1.139041 40 1.133614 41 1.133582 42 1.138309 43 1.140517 44 1.137128 45 1.145841 46 1.145623 47 1.146886 48 1.145315 49 1.151354 50 1.15735 51 1.153329 52 1.149489 53 1.147567 54 1.147828 55 1.147425 56 1.14416 57 1.141913 58 1.137349 59 1.130395 60 1.128783 61 1.132836 62 1.129102 63 1.124444 64 1.122863 65 1.125177 66 1.125448 67 1.121694 68 1.114045 69 1.107744 70 1.097176 71 1.089005 72 1.086617 73 1.076254 74 1.067765 75 1.061337 76 1.050286 77 1.033584 78 1.027984 79 1.018505 80 1.000776 81 0.98028 82 0.97195 83 0.959222 84 0.947043 85 0.940723 86 0.925592 87 0.908402 88 0.887949 89 0.868727 90 0.850103 91 0.82731 92 0.80458 93 0.778323 94 0.750454 95 0.719467 96 0.685347 97 0.648727 98 0.611911 99 0.570851 100 0.524675