## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=16wk_PBS3_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/16wk_PBS3_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 06:13:48 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 2314996356 2314907690 30470524 1439382201 548811551 111400240 184843174 0 0 0 9530237 9454400 70280 0.501997 0.498003 0.013163 0.621788 0.237077 0.048123 0.079849 0.858865 0.858832 0 0.426333 0.286654 0.267553 1.094421 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.082594 1 0.134603 2 0.236236 3 0.348844 4 0.427858 5 0.522802 6 0.606141 7 0.671043 8 0.727529 9 0.774336 10 0.816208 11 0.856873 12 0.89355 13 0.926274 14 0.952908 15 0.979446 16 1.000644 17 1.021601 18 1.038669 19 1.054321 20 1.068075 21 1.081884 22 1.098953 23 1.1116 24 1.120474 25 1.137134 26 1.146777 27 1.159909 28 1.175323 29 1.184923 30 1.188184 31 1.198353 32 1.206466 33 1.209021 34 1.21899 35 1.230185 36 1.228673 37 1.228804 38 1.232478 39 1.235728 40 1.234283 41 1.235218 42 1.22846 43 1.22349 44 1.224322 45 1.225865 46 1.226121 47 1.222106 48 1.218949 49 1.216652 50 1.220549 51 1.220643 52 1.219905 53 1.21731 54 1.215045 55 1.212686 56 1.216492 57 1.216198 58 1.215014 59 1.215931 60 1.215786 61 1.216379 62 1.211639 63 1.207642 64 1.207555 65 1.200349 66 1.192406 67 1.18395 68 1.176959 69 1.171462 70 1.169751 71 1.169561 72 1.160806 73 1.155301 74 1.149262 75 1.138945 76 1.132162 77 1.12334 78 1.111546 79 1.100731 80 1.079925 81 1.0619 82 1.047188 83 1.029541 84 1.009686 85 0.988519 86 0.963103 87 0.931773 88 0.897088 89 0.852333 90 0.80046 91 0.748199 92 0.694062 93 0.633739 94 0.560325 95 0.474683 96 0.381921 97 0.285111 98 0.187404 99 0.101068 100 0.051563