File Info
- Filename
- tih_rna_sample_00235_23H5VFLT4_s07_rna_metrics.txt
- Full Path
- s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0003/B23H5VFLT4/nfcore_rnafusion_100M__5f1fa79--20260304-100305/QC/picard/tih_rna_sample_00235_23H5VFLT4_s07_rna_metrics.txt
- Size
- 2.9 KB
- Workflow Run
- dev_rna_exp0003_5f1fa79
- Published
- Mar 04, 2026 5:47 PM
Content
View in new tab## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT tih_rna_sample_00235_23H5VFLT4_s07.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00235_23H5VFLT4_s07_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: Thu Mar 05 00:48:13 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 26011880803 25695811762 18736 21851515678 2137657672 1497618862 209000814 0 0 0 3064309 76139542 279768 0.038689 0.961311 0.000001 0.850392 0.083191 0.058283 0.008134 0.933583 0.922239 0 0.503914 0.568052 0.744266 0.864486 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.262948 1 0.305982 2 0.362527 3 0.424908 4 0.492315 5 0.561675 6 0.626151 7 0.68521 8 0.740254 9 0.801743 10 0.849464 11 0.893392 12 0.943879 13 0.985166 14 1.010889 15 1.044847 16 1.073343 17 1.104942 18 1.123836 19 1.136487 20 1.154478 21 1.177352 22 1.189117 23 1.207291 24 1.206024 25 1.204623 26 1.197671 27 1.191492 28 1.19097 29 1.186737 30 1.179204 31 1.178792 32 1.174529 33 1.17269 34 1.166766 35 1.175113 36 1.168884 37 1.15869 38 1.157744 39 1.150233 40 1.147372 41 1.149488 42 1.151868 43 1.154531 44 1.154146 45 1.162808 46 1.158913 47 1.150696 48 1.145802 49 1.145512 50 1.129546 51 1.127131 52 1.126975 53 1.12218 54 1.129202 55 1.133511 56 1.131851 57 1.136943 58 1.126025 59 1.12395 60 1.115165 61 1.117387 62 1.120131 63 1.121637 64 1.122641 65 1.127153 66 1.120321 67 1.117258 68 1.118029 69 1.112082 70 1.099262 71 1.085031 72 1.08466 73 1.080958 74 1.074069 75 1.06316 76 1.047608 77 1.037454 78 1.030423 79 1.018915 80 1.011591 81 0.998029 82 0.983257 83 0.963846 84 0.946523 85 0.924007 86 0.901459 87 0.884027 88 0.860367 89 0.837619 90 0.815506 91 0.797005 92 0.776941 93 0.745935 94 0.722601 95 0.692769 96 0.660527 97 0.628167 98 0.594774 99 0.559242 100 0.517196