RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354345.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) = 48,340,633 / 48,272,027 read pairs aligned = 48,264,211 total alignments = 103,230,966 secondary alignments = 6,618,306 non-unique alignments = 10,552,453 aligned to genes = 75,749,067 ambiguous alignments = 308,048 no feature assigned = 16,181,452 not aligned = 8,794,340 >>>>>>> Reads genomic origin exonic = 75,749,067 (82.4%) intronic = 12,716,535 (13.83%) intergenic = 3,464,917 (3.77%) overlapping exon = 3,208,859 (3.49%) >>>>>>> Transcript coverage profile 5' bias = 0.37 3' bias = 0.16 5'-3' bias = 1.92 >>>>>>> Junction analysis reads at junctions = 26,687,230 ACCT : 5.53% AGGT : 4.75% AGGA : 3.66% ATCT : 3.5% TCCT : 3.47% AGCT : 2.69% GCCT : 2.64% TTCT : 2.45% AGAT : 2.45% AGGC : 2.33% CCCT : 2.31%