File Info
- Filename
- tih_rna_sample_00377_23H5VFLT4_s23_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_00377_23H5VFLT4_s23_rna_metrics.txt
- Size
- 2.8 KB
- Workflow Run
- dev_rna_exp0003_5f1fa79
- Published
- Mar 04, 2026 5:46 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_00377_23H5VFLT4_s23.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00377_23H5VFLT4_s23_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 00:41:34 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 25519955613 24983510545 32938 21913624694 1782395056 1138347622 149110235 0 0 0 5055355 71493237 307585 0.066041 0.933959 0.000001 0.877124 0.071343 0.045564 0.005968 0.948466 0.928529 0 0.628052 0.528396 0.65051 0.960457 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.25501 1 0.302608 2 0.360052 3 0.423954 4 0.49246 5 0.559797 6 0.621461 7 0.682097 8 0.748142 9 0.811405 10 0.869939 11 0.922062 12 0.968625 13 1.015622 14 1.064722 15 1.098769 16 1.127086 17 1.151531 18 1.169075 19 1.183876 20 1.194653 21 1.207139 22 1.228873 23 1.249301 24 1.250317 25 1.246022 26 1.243138 27 1.241175 28 1.247268 29 1.243183 30 1.231243 31 1.226088 32 1.221101 33 1.213468 34 1.209494 35 1.20983 36 1.212982 37 1.213471 38 1.197793 39 1.184531 40 1.17721 41 1.174304 42 1.175887 43 1.17796 44 1.17733 45 1.180168 46 1.176916 47 1.175463 48 1.176469 49 1.174106 50 1.161458 51 1.160566 52 1.151859 53 1.145261 54 1.151486 55 1.15056 56 1.144922 57 1.135578 58 1.127981 59 1.120373 60 1.118152 61 1.113005 62 1.109149 63 1.10308 64 1.092153 65 1.092557 66 1.07509 67 1.066737 68 1.060967 69 1.049378 70 1.042024 71 1.025091 72 1.010068 73 0.997493 74 0.981246 75 0.97211 76 0.960803 77 0.957318 78 0.954096 79 0.950656 80 0.944968 81 0.93336 82 0.918968 83 0.909425 84 0.897473 85 0.885692 86 0.867729 87 0.853983 88 0.836471 89 0.813446 90 0.800337 91 0.786166 92 0.762153 93 0.733171 94 0.698288 95 0.667735 96 0.641006 97 0.611285 98 0.580832 99 0.548969 100 0.510588