## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=2wk_PBS3_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/2wk_PBS3_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 2667612303 2667506925 40079457 1619042276 660048156 118896691 229440345 0 0 0 10938893 10840923 64529 0.502249 0.497751 0.015025 0.60695 0.24744 0.044572 0.086013 0.85439 0.854356 0 0.462175 0.26011 0.295273 0.846621 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.075643 1 0.120438 2 0.205743 3 0.304213 4 0.372059 5 0.454776 6 0.528568 7 0.588141 8 0.641694 9 0.689426 10 0.730555 11 0.766962 12 0.803351 13 0.833177 14 0.858666 15 0.887966 16 0.909081 17 0.932003 18 0.949969 19 0.967015 20 0.986412 21 1.000089 22 1.015212 23 1.028674 24 1.039894 25 1.05622 26 1.067609 27 1.086537 28 1.104911 29 1.118201 30 1.124103 31 1.135635 32 1.146389 33 1.156456 34 1.160821 35 1.169565 36 1.176095 37 1.18642 38 1.190367 39 1.200376 40 1.207017 41 1.217344 42 1.223707 43 1.22249 44 1.222679 45 1.224649 46 1.23208 47 1.234232 48 1.236787 49 1.237296 50 1.239514 51 1.240937 52 1.24175 53 1.244089 54 1.249118 55 1.251145 56 1.253991 57 1.251463 58 1.253131 59 1.256844 60 1.262645 61 1.260458 62 1.255469 63 1.25535 64 1.258711 65 1.256874 66 1.246778 67 1.235339 68 1.229255 69 1.226012 70 1.223056 71 1.228332 72 1.226374 73 1.226401 74 1.220774 75 1.209673 76 1.198493 77 1.188893 78 1.179975 79 1.176421 80 1.156731 81 1.141228 82 1.127767 83 1.11596 84 1.095526 85 1.074186 86 1.040155 87 1.009318 88 0.968855 89 0.920418 90 0.871268 91 0.821022 92 0.764895 93 0.701121 94 0.622377 95 0.528911 96 0.424902 97 0.31414 98 0.20458 99 0.106718 100 0.048534