## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=Ezh12F_1_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/Ezh12F_1_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 10:57:16 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 1309391775 1309170699 263960266 529839092 195712501 157241521 162417319 0 0 0 31848 9400001 15857 0.003377 0.996623 0.201624 0.404714 0.149493 0.120108 0.124061 0.554207 0.554113 0 0.805032 0.034187 0.591641 0.060993 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.038534 1 0.04722 2 0.074721 3 0.132012 4 0.189325 5 0.277463 6 0.386937 7 0.47823 8 0.550635 9 0.593259 10 0.62759 11 0.663611 12 0.727577 13 0.757843 14 0.786918 15 0.808576 16 0.819925 17 0.840948 18 0.864717 19 0.886529 20 0.918253 21 0.94744 22 0.973331 23 0.983186 24 0.991931 25 1.006923 26 1.023268 27 1.054817 28 1.052545 29 1.04665 30 1.072173 31 1.079532 32 1.098133 33 1.107536 34 1.112764 35 1.123635 36 1.127108 37 1.135004 38 1.13798 39 1.160129 40 1.184316 41 1.187062 42 1.198661 43 1.202118 44 1.194665 45 1.181973 46 1.174112 47 1.15372 48 1.152055 49 1.163706 50 1.173082 51 1.149997 52 1.155543 53 1.192687 54 1.202247 55 1.200367 56 1.197536 57 1.186643 58 1.216034 59 1.254077 60 1.277857 61 1.253741 62 1.207721 63 1.221336 64 1.222664 65 1.219781 66 1.197007 67 1.199181 68 1.201027 69 1.183 70 1.17649 71 1.185991 72 1.187116 73 1.171847 74 1.155296 75 1.143519 76 1.162789 77 1.180039 78 1.176589 79 1.160603 80 1.154184 81 1.140989 82 1.134379 83 1.144482 84 1.165249 85 1.205797 86 1.197739 87 1.168488 88 1.163795 89 1.16489 90 1.164168 91 1.169221 92 1.160245 93 1.089293 94 1.021097 95 0.970668 96 0.8962 97 0.763192 98 0.547036 99 0.302368 100 0.102823