RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354203.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) = 33,431,998 / 33,410,133 read pairs aligned = 33,406,642 total alignments = 70,308,917 secondary alignments = 3,466,786 non-unique alignments = 5,959,437 aligned to genes = 56,532,785 ambiguous alignments = 171,928 no feature assigned = 7,476,069 not aligned = 6,873,351 >>>>>>> Reads genomic origin exonic = 56,532,785 (88.32%) intronic = 4,207,285 (6.57%) intergenic = 3,268,784 (5.11%) overlapping exon = 2,249,552 (3.51%) >>>>>>> Transcript coverage profile 5' bias = 0.24 3' bias = 0.12 5'-3' bias = 2.15 >>>>>>> Junction analysis reads at junctions = 15,522,404 ACCT : 5.52% AGGT : 4.91% AGGA : 3.75% ATCT : 3.7% TCCT : 3.46% GCCT : 3.09% AGCT : 2.72% AGGC : 2.37% AGAT : 2.37% CCCT : 2.31% TTCT : 2.18%