RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354202.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) = 39,847,832 / 39,815,823 read pairs aligned = 39,810,983 total alignments = 84,653,268 secondary alignments = 4,989,613 non-unique alignments = 8,406,337 aligned to genes = 69,070,285 ambiguous alignments = 248,188 no feature assigned = 6,615,683 not aligned = 5,957,627 >>>>>>> Reads genomic origin exonic = 69,070,285 (91.26%) intronic = 3,632,231 (4.8%) intergenic = 2,983,452 (3.94%) overlapping exon = 2,537,455 (3.35%) >>>>>>> Transcript coverage profile 5' bias = 0.32 3' bias = 0.21 5'-3' bias = 1.93 >>>>>>> Junction analysis reads at junctions = 21,507,510 ACCT : 5.44% AGGT : 4.7% TCCT : 3.66% ATCT : 3.63% AGGA : 3.36% GCCT : 3.21% AGCT : 2.64% AGGC : 2.43% CCCT : 2.42% TTCT : 2.14% AGAT : 2.06%