## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=2wk_ASNase2_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/2wk_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 06:14:31 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 2673153062 2673052685 25248044 1668295123 625305194 120454709 233749615 0 0 0 10966661 10870214 66728 0.502208 0.497792 0.009445 0.624116 0.233929 0.045063 0.087447 0.858045 0.858013 0 0.431852 0.284064 0.267204 1.053729 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.079374 1 0.130633 2 0.22772 3 0.338966 4 0.417193 5 0.509293 6 0.591428 7 0.656155 8 0.714062 9 0.764096 10 0.805552 11 0.843829 12 0.878114 13 0.909451 14 0.934327 15 0.963218 16 0.983036 17 1.005201 18 1.023631 19 1.039871 20 1.055083 21 1.065751 22 1.080924 23 1.093255 24 1.102358 25 1.117153 26 1.12408 27 1.130655 28 1.145974 29 1.157374 30 1.164628 31 1.177803 32 1.187992 33 1.19706 34 1.196933 35 1.204433 36 1.209163 37 1.21665 38 1.225421 39 1.23093 40 1.236073 41 1.242126 42 1.244908 43 1.245502 44 1.242656 45 1.239138 46 1.240648 47 1.238002 48 1.241029 49 1.240814 50 1.238678 51 1.235541 52 1.235905 53 1.236271 54 1.238478 55 1.237784 56 1.238029 57 1.234239 58 1.232605 59 1.233335 60 1.23468 61 1.229994 62 1.223101 63 1.222201 64 1.224337 65 1.218216 66 1.205462 67 1.193292 68 1.184691 69 1.177322 70 1.172574 71 1.17669 72 1.174206 73 1.168508 74 1.160495 75 1.146646 76 1.132372 77 1.12086 78 1.109154 79 1.097878 80 1.079525 81 1.067056 82 1.058068 83 1.049304 84 1.031714 85 1.009787 86 0.975702 87 0.940636 88 0.90015 89 0.854203 90 0.805348 91 0.754016 92 0.698485 93 0.635788 94 0.561941 95 0.475229 96 0.381867 97 0.282444 98 0.182617 99 0.097421 100 0.047147