RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354399.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) = 34,397,778 / 34,367,993 read pairs aligned = 34,364,255 total alignments = 73,559,242 secondary alignments = 4,793,471 non-unique alignments = 7,789,852 aligned to genes = 56,554,545 ambiguous alignments = 201,027 no feature assigned = 8,622,371 not aligned = 3,216,021 >>>>>>> Reads genomic origin exonic = 56,554,545 (86.77%) intronic = 5,942,717 (9.12%) intergenic = 2,679,654 (4.11%) overlapping exon = 2,017,978 (3.1%) >>>>>>> Transcript coverage profile 5' bias = 0.44 3' bias = 0.21 5'-3' bias = 1.98 >>>>>>> Junction analysis reads at junctions = 18,641,697 ACCT : 5.3% AGGT : 4.65% ATCT : 3.57% AGGA : 3.51% TCCT : 3.4% GCCT : 3.14% AGCT : 2.76% TTCT : 2.59% CCCT : 2.38% AGGC : 2.31% AGAT : 2.25%