## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT V4_0001_RNA_0005_23H5VFLT4_s22.Aligned.sortedByCoord.out.bam --OUTPUT V4_0001_RNA_0005_23H5VFLT4_s22_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 Mar 04 22:56:37 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 25401980097 24994021654 41389 19540116939 2447409437 2627365663 379088226 0 0 0 3131330 69057107 355454 0.043377 0.956623 0.000002 0.781792 0.09792 0.10512 0.015167 0.879711 0.865583 0 0.520831 0.572035 0.737087 0.838328 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.291151 1 0.329944 2 0.393528 3 0.461308 4 0.52929 5 0.596259 6 0.6614 7 0.722143 8 0.776253 9 0.828478 10 0.868421 11 0.913298 12 0.959357 13 0.997248 14 1.027561 15 1.056047 16 1.073501 17 1.089361 18 1.095779 19 1.112538 20 1.131202 21 1.148846 22 1.168144 23 1.182419 24 1.192831 25 1.198149 26 1.199571 27 1.199969 28 1.200056 29 1.19912 30 1.194048 31 1.194264 32 1.182866 33 1.178929 34 1.172652 35 1.168154 36 1.166586 37 1.159439 38 1.150306 39 1.144181 40 1.137646 41 1.133796 42 1.133098 43 1.129382 44 1.128343 45 1.135363 46 1.13124 47 1.124712 48 1.126474 49 1.127347 50 1.130618 51 1.127457 52 1.124599 53 1.127449 54 1.129474 55 1.129002 56 1.130621 57 1.125773 58 1.12386 59 1.120298 60 1.120622 61 1.125113 62 1.122409 63 1.119032 64 1.115951 65 1.117107 66 1.111858 67 1.106583 68 1.098047 69 1.089909 70 1.079152 71 1.070102 72 1.066755 73 1.057454 74 1.054487 75 1.045387 76 1.036098 77 1.022174 78 1.015592 79 1.004468 80 0.987077 81 0.9707 82 0.962277 83 0.946519 84 0.933449 85 0.927342 86 0.912165 87 0.892945 88 0.871721 89 0.850879 90 0.830904 91 0.810448 92 0.792464 93 0.771116 94 0.746417 95 0.719333 96 0.687383 97 0.654375 98 0.620487 99 0.581935 100 0.535956