## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=8wk_ASNase2_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/8wk_ASNase2_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 2681411832 2681304193 55327865 1641064461 650213661 115142878 219555328 0 0 0 10996972 10904652 83187 0.502108 0.497892 0.020635 0.61204 0.242499 0.042943 0.081884 0.854539 0.854504 0 0.425075 0.295204 0.253648 1.17835 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.084815 1 0.141922 2 0.247758 3 0.363275 4 0.443747 5 0.540442 6 0.623727 7 0.688235 8 0.745319 9 0.79296 10 0.833573 11 0.869726 12 0.905623 13 0.938843 14 0.966021 15 0.993536 16 1.014444 17 1.038313 18 1.056587 19 1.072616 20 1.09276 21 1.108153 22 1.125349 23 1.136505 24 1.143848 25 1.158175 26 1.169186 27 1.180021 28 1.192553 29 1.202952 30 1.209285 31 1.221012 32 1.230166 33 1.23423 34 1.243717 35 1.252017 36 1.247761 37 1.248764 38 1.250175 39 1.250851 40 1.249966 41 1.24867 42 1.243187 43 1.238348 44 1.237271 45 1.235329 46 1.23734 47 1.236161 48 1.23442 49 1.23198 50 1.231148 51 1.22584 52 1.220893 53 1.220609 54 1.219604 55 1.217764 56 1.219106 57 1.216953 58 1.215455 59 1.217163 60 1.216578 61 1.211395 62 1.202788 63 1.1969 64 1.19245 65 1.180466 66 1.171771 67 1.164839 68 1.157403 69 1.149609 70 1.142958 71 1.139573 72 1.131946 73 1.127743 74 1.117983 75 1.108272 76 1.100715 77 1.090953 78 1.080025 79 1.072007 80 1.050901 81 1.035246 82 1.022223 83 1.004512 84 0.98475 85 0.962529 86 0.938735 87 0.907184 88 0.868954 89 0.821912 90 0.772582 91 0.721875 92 0.669216 93 0.609186 94 0.538448 95 0.455666 96 0.365147 97 0.271553 98 0.177118 99 0.096021 100 0.04933