RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354135.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) = 32,907,421 / 32,881,427 read pairs aligned = 32,877,541 total alignments = 69,879,120 secondary alignments = 4,090,272 non-unique alignments = 6,767,039 aligned to genes = 54,390,617 ambiguous alignments = 186,582 no feature assigned = 8,221,258 not aligned = 5,995,000 >>>>>>> Reads genomic origin exonic = 54,390,617 (86.87%) intronic = 5,504,175 (8.79%) intergenic = 2,717,083 (4.34%) overlapping exon = 2,218,566 (3.54%) >>>>>>> Transcript coverage profile 5' bias = 0.34 3' bias = 0.2 5'-3' bias = 1.89 >>>>>>> Junction analysis reads at junctions = 17,881,100 ACCT : 5.33% AGGT : 4.74% ATCT : 3.62% AGGA : 3.58% TCCT : 3.55% GCCT : 3.2% AGCT : 2.73% CCCT : 2.52% AGGC : 2.38% AGAT : 2.28% TTCT : 2.1%