## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=M2WTM_2_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/M2WTM_2_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 10:57:14 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 1284935475 1284777327 230764382 572509959 237485768 52047238 191969980 0 0 0 25388 10456946 24584 0.002422 0.997578 0.179614 0.44561 0.184846 0.040511 0.149419 0.630456 0.630379 0 0.860792 0.030958 0.747317 0.045377 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.03219 1 0.041653 2 0.070543 3 0.125564 4 0.16515 5 0.241985 6 0.34107 7 0.419083 8 0.481358 9 0.545681 10 0.58744 11 0.621699 12 0.68892 13 0.731528 14 0.768321 15 0.77757 16 0.785984 17 0.811432 18 0.842319 19 0.865562 20 0.903452 21 0.938886 22 0.933314 23 0.956597 24 0.970771 25 0.997449 26 1.026601 27 1.056356 28 1.075845 29 1.058439 30 1.074298 31 1.073982 32 1.098056 33 1.104747 34 1.145573 35 1.150577 36 1.160593 37 1.161417 38 1.143161 39 1.133117 40 1.143675 41 1.162872 42 1.168697 43 1.171179 44 1.168543 45 1.167856 46 1.164073 47 1.141252 48 1.135807 49 1.145253 50 1.149804 51 1.133472 52 1.140693 53 1.157924 54 1.168206 55 1.17841 56 1.178197 57 1.180034 58 1.222126 59 1.25279 60 1.258617 61 1.228581 62 1.19588 63 1.19343 64 1.179232 65 1.188903 66 1.166444 67 1.153592 68 1.15009 69 1.135513 70 1.142988 71 1.170187 72 1.168154 73 1.18643 74 1.152312 75 1.142524 76 1.145745 77 1.162664 78 1.156129 79 1.1376 80 1.125341 81 1.127774 82 1.145962 83 1.154087 84 1.164028 85 1.188305 86 1.191055 87 1.200222 88 1.232443 89 1.255286 90 1.236379 91 1.231717 92 1.229263 93 1.187334 94 1.140095 95 1.097729 96 1.060169 97 0.956167 98 0.750003 99 0.459467 100 0.175042