## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=8wk_PBS3_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/8wk_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 3014617902 3014506923 50403374 1883954728 734381269 104222464 241545088 0 0 0 12584682 12455835 86940 0.502573 0.497427 0.01672 0.624963 0.243616 0.034574 0.080128 0.868579 0.868547 0 0.438246 0.289666 0.260997 1.098275 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.080367 1 0.130333 2 0.228482 3 0.339469 4 0.420011 5 0.517192 6 0.600404 7 0.665576 8 0.72148 9 0.769085 10 0.808763 11 0.844787 12 0.878794 13 0.911723 14 0.938271 15 0.964822 16 0.983696 17 1.005047 18 1.023531 19 1.038902 20 1.055636 21 1.069406 22 1.083522 23 1.095116 24 1.105854 25 1.119892 26 1.130956 27 1.143873 28 1.157375 29 1.167224 30 1.171674 31 1.181296 32 1.189905 33 1.193708 34 1.21399 35 1.225834 36 1.219669 37 1.219772 38 1.220498 39 1.223431 40 1.224593 41 1.233737 42 1.236314 43 1.235755 44 1.232777 45 1.231351 46 1.233853 47 1.232226 48 1.230562 49 1.230169 50 1.231912 51 1.229838 52 1.227215 53 1.22743 54 1.228175 55 1.226963 56 1.22897 57 1.228641 58 1.231164 59 1.233517 60 1.235177 61 1.233434 62 1.227738 63 1.223408 64 1.222483 65 1.214683 66 1.206079 67 1.200821 68 1.194074 69 1.186896 70 1.181515 71 1.179158 72 1.171161 73 1.165374 74 1.158026 75 1.146788 76 1.13926 77 1.128097 78 1.116914 79 1.107692 80 1.085439 81 1.067029 82 1.053768 83 1.034062 84 1.015059 85 0.993385 86 0.9689 87 0.937358 88 0.900965 89 0.85436 90 0.805474 91 0.756444 92 0.702531 93 0.637716 94 0.563747 95 0.476607 96 0.377876 97 0.276704 98 0.177816 99 0.091228 100 0.042261