File Info
- Filename
- SS_FFPE_V4_0001_RNA_0011_23LGNLLT4_1_rna_metrics.txt
- Full Path
- s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0005/A23LGNLLT4/nfcore_rnafusion__2cae617--20260515-145204/QC/picard/SS_FFPE_V4_0001_RNA_0011_23LGNLLT4_1_rna_metrics.txt
- Size
- 2.9 KB
- Workflow Run
- dev_rna_exp0005_2cae617
- Published
- May 16, 2026 6:05 AM
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 SS_FFPE_V4_0001_RNA_0011_23LGNLLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT SS_FFPE_V4_0001_RNA_0011_23LGNLLT4_1_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: Sat May 16 09:39:45 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 77289196704 76412656055 41330 65107887677 6590267093 4167913776 546546179 0 0 0 5052602 229386707 1566776 0.021552 0.978448 0.000001 0.852056 0.086246 0.054545 0.007153 0.938302 0.927661 0 0.502722 0.590841 0.770914 0.870931 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.265307 1 0.305029 2 0.364772 3 0.430033 4 0.498144 5 0.564391 6 0.628489 7 0.688213 8 0.739982 9 0.788478 10 0.831883 11 0.878252 12 0.926924 13 0.970624 14 1.003443 15 1.03283 16 1.057967 17 1.071806 18 1.086312 19 1.102937 20 1.12251 21 1.141226 22 1.153552 23 1.164008 24 1.174341 25 1.179629 26 1.184021 27 1.188875 28 1.188277 29 1.183277 30 1.176847 31 1.176084 32 1.165443 33 1.163552 34 1.161962 35 1.164208 36 1.167361 37 1.157089 38 1.146446 39 1.14864 40 1.145848 41 1.14555 42 1.145719 43 1.14522 44 1.144873 45 1.152052 46 1.147554 47 1.148054 48 1.147076 49 1.152428 50 1.157408 51 1.154446 52 1.15174 53 1.15231 54 1.150285 55 1.147218 56 1.142815 57 1.13895 58 1.135887 59 1.131162 60 1.129555 61 1.128427 62 1.124828 63 1.120248 64 1.116709 65 1.114725 66 1.108233 67 1.106247 68 1.099635 69 1.093916 70 1.085534 71 1.078731 72 1.077232 73 1.073785 74 1.068775 75 1.062212 76 1.050821 77 1.039595 78 1.035052 79 1.025655 80 1.006211 81 0.989061 82 0.981208 83 0.964921 84 0.952072 85 0.94476 86 0.929191 87 0.920904 88 0.903495 89 0.883752 90 0.859394 91 0.834241 92 0.809846 93 0.776797 94 0.747142 95 0.715532 96 0.680249 97 0.643615 98 0.607792 99 0.566897 100 0.520968