## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=16wk_ASNase3_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/16wk_ASNase3_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 06:13:47 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 2357066088 2356844340 362193897 1237407238 506108405 94847597 156287203 0 0 0 8367365 8287305 58529 0.502404 0.497596 0.153677 0.525027 0.21474 0.040243 0.066312 0.739767 0.739697 0 0.452194 0.262965 0.271783 0.993091 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.079966 1 0.128724 2 0.221923 3 0.3195 4 0.385784 5 0.46968 6 0.545 7 0.601352 8 0.65532 9 0.700266 10 0.738953 11 0.775475 12 0.810703 13 0.845469 14 0.872852 15 0.900441 16 0.92007 17 0.941755 18 0.962069 19 0.982141 20 1.004264 21 1.020502 22 1.037665 23 1.050782 24 1.062088 25 1.078603 26 1.091274 27 1.104059 28 1.116132 29 1.126465 30 1.13266 31 1.146669 32 1.155041 33 1.159136 34 1.174197 35 1.190044 36 1.191781 37 1.195571 38 1.199736 39 1.207787 40 1.214707 41 1.223627 42 1.225504 43 1.226758 44 1.228445 45 1.228036 46 1.229359 47 1.233783 48 1.235981 49 1.239265 50 1.243355 51 1.242807 52 1.238798 53 1.240581 54 1.245454 55 1.247406 56 1.25289 57 1.255092 58 1.257171 59 1.258144 60 1.261234 61 1.264419 62 1.258429 63 1.258805 64 1.259958 65 1.252757 66 1.244334 67 1.238106 68 1.228821 69 1.221465 70 1.216686 71 1.216782 72 1.211452 73 1.207194 74 1.199182 75 1.188737 76 1.182585 77 1.172167 78 1.162343 79 1.154543 80 1.135268 81 1.119044 82 1.105635 83 1.08873 84 1.06955 85 1.047078 86 1.018935 87 0.98663 88 0.950412 89 0.906072 90 0.855818 91 0.804726 92 0.746589 93 0.679139 94 0.600169 95 0.507032 96 0.403309 97 0.297516 98 0.192052 99 0.101642 100 0.048155