## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=WTM_3_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/WTM_3_metrics MINIMUM_LENGTH=500 RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] 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 GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader # Started on: Mon Mar 09 10:54:31 EDT 2020 ## 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 1562030625 1561886823 303577665 721919798 220936654 148633204 166819502 0 0 0 29975 12202777 19690 0.00245 0.99755 0.194366 0.46221 0.141455 0.095163 0.106806 0.603665 0.603609 0 0.691811 0.048966 0.664382 0.083705 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.0412 1 0.053772 2 0.090918 3 0.153932 4 0.218558 5 0.326003 6 0.444579 7 0.545099 8 0.615203 9 0.659316 10 0.694697 11 0.725915 12 0.784484 13 0.81646 14 0.854673 15 0.884016 16 0.885964 17 0.910861 18 0.934068 19 0.963349 20 0.999485 21 1.023323 22 1.03995 23 1.058088 24 1.072747 25 1.088518 26 1.094945 27 1.133081 28 1.141351 29 1.136707 30 1.161924 31 1.159995 32 1.168981 33 1.174098 34 1.187416 35 1.200401 36 1.207301 37 1.205876 38 1.184414 39 1.193328 40 1.21218 41 1.220461 42 1.234956 43 1.240021 44 1.231733 45 1.216807 46 1.215285 47 1.188255 48 1.174388 49 1.184107 50 1.18585 51 1.15736 52 1.150703 53 1.18508 54 1.195421 55 1.193253 56 1.183672 57 1.177523 58 1.208591 59 1.232103 60 1.244379 61 1.218255 62 1.168546 63 1.177768 64 1.184266 65 1.187159 66 1.147263 67 1.12601 68 1.119387 69 1.118009 70 1.117346 71 1.129869 72 1.13407 73 1.121486 74 1.100389 75 1.084371 76 1.084679 77 1.105585 78 1.110088 79 1.09892 80 1.088636 81 1.057825 82 1.043271 83 1.055588 84 1.066284 85 1.084314 86 1.071108 87 1.054139 88 1.058513 89 1.047606 90 1.039576 91 1.042849 92 1.030943 93 0.981189 94 0.936173 95 0.898426 96 0.8422 97 0.74178 98 0.562494 99 0.325064 100 0.111401