RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354172.markdup.sorted.bam gff file = gencode.v44.annotation_genes_collapsed_only_patched_ERCC92.gtf counting algorithm = uniquely-mapped-reads protocol = strand-specific-reverse 5'-3' bias region size = 100 5'-3' bias number of top transcripts = 1000 >>>>>>> Reads alignment reads aligned (left/right) = 31,107,863 / 31,086,424 read pairs aligned = 31,082,532 total alignments = 65,994,299 secondary alignments = 3,800,012 non-unique alignments = 6,251,368 aligned to genes = 51,897,122 ambiguous alignments = 175,611 no feature assigned = 7,350,117 not aligned = 3,049,015 >>>>>>> Reads genomic origin exonic = 51,897,122 (87.59%) intronic = 4,787,409 (8.08%) intergenic = 2,562,708 (4.33%) overlapping exon = 2,136,688 (3.61%) >>>>>>> Transcript coverage profile 5' bias = 0.38 3' bias = 0.19 5'-3' bias = 2.17 >>>>>>> Junction analysis reads at junctions = 15,742,232 ACCT : 5.47% AGGT : 4.76% ATCT : 3.71% AGGA : 3.54% TCCT : 3.49% GCCT : 3.08% AGCT : 2.71% CCCT : 2.45% AGGC : 2.36% AGAT : 2.21% TTCT : 2.1%