## 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_42.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_42_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 17:59:54 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 25097340316 24810676087 14142 21666385681 2007020030 1005280030 131976204 0 0 0 1131846 78573369 342379 0.0142 0.9858 0.000001 0.873269 0.080893 0.040518 0.005319 0.954162 0.943264 0 0.514239 0.559989 0.761969 0.823531 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.269639 1 0.307991 2 0.364435 3 0.429336 4 0.49766 5 0.564622 6 0.626455 7 0.686077 8 0.74224 9 0.795916 10 0.84175 11 0.892121 12 0.945699 13 0.986935 14 1.017585 15 1.043558 16 1.059291 17 1.071999 18 1.08481 19 1.099048 20 1.109357 21 1.128422 22 1.140445 23 1.152568 24 1.162303 25 1.165221 26 1.171129 27 1.177534 28 1.179141 29 1.175384 30 1.169421 31 1.167265 32 1.155617 33 1.152797 34 1.147737 35 1.146227 36 1.147614 37 1.140086 38 1.133021 39 1.132004 40 1.127661 41 1.126799 42 1.13119 43 1.134228 44 1.135767 45 1.145445 46 1.146732 47 1.147703 48 1.147152 49 1.154033 50 1.16217 51 1.16351 52 1.161357 53 1.161385 54 1.162549 55 1.16389 56 1.160377 57 1.160466 58 1.157982 59 1.150252 60 1.14519 61 1.144184 62 1.14148 63 1.136899 64 1.135249 65 1.137128 66 1.133856 67 1.129426 68 1.121547 69 1.114537 70 1.10516 71 1.099648 72 1.095795 73 1.085734 74 1.077186 75 1.069813 76 1.056957 77 1.038095 78 1.031082 79 1.020418 80 1.002662 81 0.981551 82 0.972473 83 0.958709 84 0.9452 85 0.938073 86 0.923634 87 0.906608 88 0.882158 89 0.862204 90 0.843493 91 0.821932 92 0.800393 93 0.773292 94 0.741772 95 0.707471 96 0.673634 97 0.639735 98 0.603395 99 0.563645 100 0.518438