## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=8wk_ASNase3_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/8wk_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 06:13:48 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 2921344099 2921167415 233544152 1691192031 657788493 107428709 231214030 0 0 0 11278597 11189615 77820 0.50198 0.49802 0.079949 0.578944 0.22518 0.036776 0.079151 0.804124 0.804075 0 0.428963 0.284804 0.248426 1.148248 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.082643 1 0.136839 2 0.241559 3 0.356709 4 0.437342 5 0.535648 6 0.619488 7 0.685352 8 0.744255 9 0.794118 10 0.83652 11 0.875 12 0.909336 13 0.94139 14 0.967395 15 0.9967 16 1.017325 17 1.040342 18 1.058621 19 1.073589 20 1.09209 21 1.108687 22 1.125579 23 1.137361 24 1.146924 25 1.159377 26 1.169077 27 1.180156 28 1.193257 29 1.203938 30 1.208664 31 1.22283 32 1.233693 33 1.238403 34 1.249827 35 1.257045 36 1.251026 37 1.248841 38 1.25053 39 1.251415 40 1.249181 41 1.247028 42 1.241524 43 1.237207 44 1.233955 45 1.233114 46 1.232529 47 1.230071 48 1.23107 49 1.229398 50 1.228843 51 1.224526 52 1.218409 53 1.217524 54 1.216312 55 1.215254 56 1.218769 57 1.216814 58 1.218581 59 1.22091 60 1.221523 61 1.217715 62 1.208816 63 1.201613 64 1.196743 65 1.184839 66 1.173682 67 1.163369 68 1.156226 69 1.151185 70 1.14669 71 1.14452 72 1.13727 73 1.131888 74 1.119173 75 1.105812 76 1.099838 77 1.091718 78 1.083068 79 1.073102 80 1.051136 81 1.03468 82 1.022044 83 1.004645 84 0.984613 85 0.960827 86 0.934412 87 0.903143 88 0.866156 89 0.820859 90 0.771686 91 0.72187 92 0.669117 93 0.609689 94 0.537202 95 0.452854 96 0.361955 97 0.267848 98 0.173164 99 0.091412 100 0.045516