File Info
- Filename
- tih_rna_sample_00272_23H5VFLT4_s09_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_00272_23H5VFLT4_s09_rna_metrics.txt
- Size
- 2.8 KB
- Workflow Run
- dev_rna_exp0003_5f1fa79
- Published
- Mar 04, 2026 5:31 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_00272_23H5VFLT4_s09.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00272_23H5VFLT4_s09_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 23:55:35 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 25805200114 25506242121 17521 21828441143 1838994518 1649145320 189643619 0 0 0 2819612 76753798 259932 0.035434 0.964566 0.000001 0.855808 0.0721 0.064657 0.007435 0.927908 0.917158 0 0.496601 0.544974 0.758678 0.8293 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.316684 1 0.350029 2 0.394938 3 0.451095 4 0.505808 5 0.555852 6 0.615246 7 0.673426 8 0.725502 9 0.773303 10 0.818502 11 0.864649 12 0.907907 13 0.944146 14 0.976893 15 1.015821 16 1.032096 17 1.045315 18 1.062323 19 1.077438 20 1.098637 21 1.115457 22 1.131882 23 1.149265 24 1.158552 25 1.163309 26 1.166111 27 1.171331 28 1.172725 29 1.16908 30 1.169893 31 1.16589 32 1.166248 33 1.169126 34 1.169307 35 1.173891 36 1.173692 37 1.169475 38 1.168869 39 1.173757 40 1.171556 41 1.169817 42 1.170878 43 1.173113 44 1.174036 45 1.175651 46 1.173393 47 1.17998 48 1.181754 49 1.183236 50 1.178777 51 1.170877 52 1.163582 53 1.154001 54 1.154271 55 1.151616 56 1.149246 57 1.141182 58 1.130663 59 1.122242 60 1.116884 61 1.124532 62 1.126882 63 1.129597 64 1.128943 65 1.12306 66 1.117878 67 1.109126 68 1.095902 69 1.091575 70 1.082697 71 1.072696 72 1.06214 73 1.055886 74 1.046802 75 1.038546 76 1.032521 77 1.02505 78 1.022613 79 1.019037 80 1.009853 81 0.997901 82 0.99132 83 0.977926 84 0.960658 85 0.943718 86 0.921302 87 0.905599 88 0.883778 89 0.863674 90 0.844304 91 0.822313 92 0.799487 93 0.773639 94 0.747573 95 0.721876 96 0.695371 97 0.662536 98 0.627006 99 0.59368 100 0.550895