## 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_10.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_10_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 17:59:17 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 25370269613 25082106445 8767 21923241073 2038419642 984064679 136372284 0 0 0 2050600 77846351 315605 0.025666 0.974334 0 0.874059 0.08127 0.039234 0.005437 0.955329 0.944478 0 0.506907 0.5873 0.751359 0.881628 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.269558 1 0.309135 2 0.368933 3 0.436334 4 0.506973 5 0.576129 6 0.639871 7 0.701908 8 0.758255 9 0.812641 10 0.858999 11 0.906598 12 0.957104 13 1.000101 14 1.031186 15 1.05676 16 1.080431 17 1.097575 18 1.116114 19 1.13128 20 1.141627 21 1.158081 22 1.167449 23 1.176812 24 1.184889 25 1.186549 26 1.192376 27 1.197687 28 1.196597 29 1.192157 30 1.186323 31 1.18044 32 1.166279 33 1.16323 34 1.156624 35 1.155243 36 1.157003 37 1.15001 38 1.139765 39 1.13559 40 1.130286 41 1.128597 42 1.13246 43 1.134558 44 1.130381 45 1.141526 46 1.142855 47 1.142183 48 1.143118 49 1.149738 50 1.158001 51 1.156734 52 1.15362 53 1.152272 54 1.150335 55 1.152134 56 1.148461 57 1.148287 58 1.144611 59 1.13497 60 1.130793 61 1.131903 62 1.127128 63 1.119592 64 1.117462 65 1.118666 66 1.117129 67 1.111768 68 1.102847 69 1.094994 70 1.086636 71 1.079959 72 1.075604 73 1.066166 74 1.058525 75 1.051643 76 1.040738 77 1.02125 78 1.013486 79 1.003907 80 0.986579 81 0.967736 82 0.960549 83 0.948471 84 0.937444 85 0.931343 86 0.917384 87 0.901577 88 0.879379 89 0.858436 90 0.840931 91 0.818177 92 0.795246 93 0.76697 94 0.735474 95 0.700808 96 0.666604 97 0.63196 98 0.596125 99 0.557234 100 0.513149