## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=M2WTF_1_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/M2WTF_1_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 10:56:45 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 1515099675 1514986175 150294118 714754311 274308803 118995279 256633664 0 0 0 36241 12725807 30037 0.00284 0.99716 0.099205 0.471789 0.181064 0.078545 0.169397 0.652853 0.652804 0 0.85427 0.027853 0.73 0.045611 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.032146 1 0.044535 2 0.078193 3 0.130309 4 0.172545 5 0.254464 6 0.352978 7 0.436871 8 0.507391 9 0.566418 10 0.604443 11 0.632763 12 0.701761 13 0.742992 14 0.775633 15 0.794307 16 0.81014 17 0.835615 18 0.866277 19 0.889703 20 0.919631 21 0.943893 22 0.953857 23 0.983107 24 0.992355 25 1.00747 26 1.027371 27 1.065165 28 1.088816 29 1.063933 30 1.066085 31 1.06669 32 1.081603 33 1.083422 34 1.127968 35 1.143237 36 1.151991 37 1.160826 38 1.147138 39 1.144192 40 1.157958 41 1.183372 42 1.19372 43 1.208683 44 1.207696 45 1.188086 46 1.176175 47 1.133277 48 1.126269 49 1.151496 50 1.15411 51 1.134351 52 1.127157 53 1.141382 54 1.161338 55 1.172599 56 1.176746 57 1.186618 58 1.217019 59 1.235024 60 1.238813 61 1.211036 62 1.175598 63 1.174991 64 1.186588 65 1.211926 66 1.19976 67 1.172086 68 1.167696 69 1.148047 70 1.143586 71 1.158495 72 1.152437 73 1.1612 74 1.133168 75 1.125002 76 1.126622 77 1.139699 78 1.149942 79 1.135704 80 1.128916 81 1.127113 82 1.138854 83 1.138567 84 1.153117 85 1.183835 86 1.175258 87 1.173513 88 1.205468 89 1.233256 90 1.210099 91 1.190783 92 1.196983 93 1.154196 94 1.115062 95 1.073964 96 1.030156 97 0.93688 98 0.745222 99 0.470239 100 0.190108