## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=8wk_PBS2_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/8wk_PBS2_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 06:14:26 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 2427751140 2427656410 34237307 1536777347 572055369 85245442 199340945 0 0 0 10108749 10058602 76821 0.501243 0.498757 0.014103 0.633029 0.235641 0.035114 0.082113 0.86867 0.868636 0 0.423754 0.307719 0.246227 1.184005 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.082811 1 0.140736 2 0.253247 3 0.377439 4 0.46592 5 0.569716 6 0.658756 7 0.724964 8 0.782581 9 0.830013 10 0.869146 11 0.905969 12 0.942906 13 0.977897 14 1.004859 15 1.033395 16 1.053158 17 1.074261 18 1.091631 19 1.106902 20 1.124235 21 1.139212 22 1.152007 23 1.161716 24 1.168826 25 1.180741 26 1.189138 27 1.200683 28 1.213629 29 1.223791 30 1.228395 31 1.241347 32 1.249755 33 1.251549 34 1.261107 35 1.268573 36 1.260071 37 1.25769 38 1.258885 39 1.259299 40 1.259376 41 1.260109 42 1.253864 43 1.246897 44 1.241256 45 1.234909 46 1.233863 47 1.230916 48 1.226126 49 1.223025 50 1.220693 51 1.215323 52 1.209883 53 1.206929 54 1.204957 55 1.202922 56 1.202338 57 1.196299 58 1.194764 59 1.193155 60 1.191903 61 1.188995 62 1.18241 63 1.17806 64 1.175857 65 1.166575 66 1.156847 67 1.145997 68 1.136246 69 1.12923 70 1.123853 71 1.118691 72 1.109792 73 1.104136 74 1.095881 75 1.085127 76 1.075468 77 1.064783 78 1.053315 79 1.041784 80 1.020008 81 1.002557 82 0.989879 83 0.971955 84 0.954108 85 0.932551 86 0.907341 87 0.877568 88 0.843379 89 0.801015 90 0.755135 91 0.707983 92 0.656979 93 0.596633 94 0.52681 95 0.44473 96 0.355565 97 0.263225 98 0.170589 99 0.090897 100 0.045699