RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354208.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) = 56,228,801 / 56,155,407 read pairs aligned = 56,130,702 total alignments = 120,547,792 secondary alignments = 8,163,584 non-unique alignments = 12,342,100 aligned to genes = 92,451,525 ambiguous alignments = 371,631 no feature assigned = 14,209,486 not aligned = 2,411,982 >>>>>>> Reads genomic origin exonic = 92,451,525 (86.68%) intronic = 10,235,938 (9.6%) intergenic = 3,973,548 (3.73%) overlapping exon = 4,896,593 (4.59%) >>>>>>> Transcript coverage profile 5' bias = 0.49 3' bias = 0.24 5'-3' bias = 1.73 >>>>>>> Junction analysis reads at junctions = 35,158,914 ACCT : 5.27% AGGT : 4.7% ATCT : 3.7% TCCT : 3.42% AGGA : 3.36% GCCT : 3.33% CCCT : 2.83% AGCT : 2.7% AGGC : 2.42% TTCT : 2.16% AGAT : 2.07%