RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354246.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) = 43,248,477 / 43,222,205 read pairs aligned = 43,208,977 total alignments = 93,399,191 secondary alignments = 6,928,509 non-unique alignments = 11,487,446 aligned to genes = 73,091,054 ambiguous alignments = 271,737 no feature assigned = 7,993,070 not aligned = 5,187,670 >>>>>>> Reads genomic origin exonic = 73,091,054 (90.14%) intronic = 5,307,546 (6.55%) intergenic = 2,685,524 (3.31%) overlapping exon = 3,570,643 (4.4%) >>>>>>> Transcript coverage profile 5' bias = 0.24 3' bias = 0.16 5'-3' bias = 2.28 >>>>>>> Junction analysis reads at junctions = 23,805,056 ACCT : 5.14% AGGT : 4.81% ATCT : 4.22% TCCT : 3.88% AGGA : 3.31% GCCT : 2.97% CCCT : 2.76% AGCT : 2.38% AGGC : 2.31% TTCT : 2.14% AGAA : 2%