## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=2wk_PBS1_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/2wk_PBS1_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 06:13:47 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 2573438489 2573313911 45376680 1546074988 626284676 124449276 231128291 0 0 0 10485896 10349662 72367 0.503269 0.496731 0.017634 0.600811 0.243377 0.048361 0.089817 0.844188 0.844147 0 0.443567 0.270361 0.293242 0.919508 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.079306 1 0.130051 2 0.223174 3 0.327791 4 0.396356 5 0.480987 6 0.557207 7 0.617965 8 0.672592 9 0.716753 10 0.755335 11 0.790572 12 0.824905 13 0.857249 14 0.882981 15 0.90788 16 0.927697 17 0.947281 18 0.964553 19 0.979775 20 0.997574 21 1.012446 22 1.027465 23 1.039697 24 1.049101 25 1.062324 26 1.0728 27 1.083972 28 1.100247 29 1.109744 30 1.117468 31 1.131972 32 1.141704 33 1.151841 34 1.154196 35 1.163455 36 1.169615 37 1.17945 38 1.191054 39 1.201368 40 1.20998 41 1.222424 42 1.225508 43 1.226 44 1.224694 45 1.225503 46 1.230584 47 1.230899 48 1.232082 49 1.233952 50 1.235609 51 1.237032 52 1.231086 53 1.230915 54 1.232761 55 1.233763 56 1.237549 57 1.23624 58 1.239704 59 1.244597 60 1.248467 61 1.248245 62 1.245738 63 1.243766 64 1.245854 65 1.24077 66 1.234284 67 1.227467 68 1.221217 69 1.21794 70 1.217225 71 1.218698 72 1.212802 73 1.209396 74 1.199947 75 1.190293 76 1.185336 77 1.17631 78 1.16386 79 1.15512 80 1.138286 81 1.130712 82 1.118613 83 1.09976 84 1.07945 85 1.058775 86 1.033624 87 1.006329 88 0.969399 89 0.924454 90 0.87635 91 0.825393 92 0.770496 93 0.70529 94 0.625905 95 0.533414 96 0.429091 97 0.318528 98 0.206699 99 0.109359 100 0.051749