## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=Ezh12M_2_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/Ezh12M_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 10:57:16 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 1422295650 1422146607 216888861 775231985 214202535 74082327 141740899 0 0 0 20468 12854572 17266 0.00159 0.99841 0.152508 0.545114 0.150619 0.052092 0.099667 0.695733 0.69566 0 0.918163 0.03422 0.376814 0.08589 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.035217 1 0.043046 2 0.080167 3 0.151336 4 0.21749 5 0.320647 6 0.448119 7 0.538858 8 0.60559 9 0.642976 10 0.68517 11 0.739976 12 0.834805 13 0.8657 14 0.891575 15 0.918658 16 0.939954 17 0.955699 18 0.973384 19 0.985168 20 1.001532 21 1.023882 22 1.052931 23 1.052069 24 1.080529 25 1.100492 26 1.121168 27 1.1444 28 1.132857 29 1.117929 30 1.133115 31 1.148035 32 1.177636 33 1.191948 34 1.192848 35 1.190027 36 1.196872 37 1.20242 38 1.198257 39 1.229448 40 1.249658 41 1.240247 42 1.240279 43 1.249572 44 1.226772 45 1.202603 46 1.187155 47 1.178764 48 1.199439 49 1.224781 50 1.224192 51 1.188384 52 1.172921 53 1.199317 54 1.213001 55 1.200636 56 1.199469 57 1.201825 58 1.235095 59 1.271602 60 1.261797 61 1.212621 62 1.174955 63 1.192879 64 1.192918 65 1.201325 66 1.173232 67 1.163398 68 1.154999 69 1.128657 70 1.126486 71 1.129683 72 1.133546 73 1.127361 74 1.115612 75 1.102931 76 1.091774 77 1.08948 78 1.076099 79 1.061425 80 1.069773 81 1.064184 82 1.055334 83 1.068264 84 1.079115 85 1.106912 86 1.08888 87 1.064595 88 1.062882 89 1.048732 90 1.02127 91 1.019969 92 0.996019 93 0.931715 94 0.869392 95 0.807389 96 0.720094 97 0.588392 98 0.399871 99 0.208277 100 0.068245