RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354110.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) = 42,220,712 / 42,025,629 read pairs aligned = 41,988,929 total alignments = 91,067,854 secondary alignments = 6,821,513 non-unique alignments = 10,991,058 aligned to genes = 59,990,235 ambiguous alignments = 187,634 no feature assigned = 19,249,321 not aligned = 18,192,759 >>>>>>> Reads genomic origin exonic = 59,990,235 (75.71%) intronic = 9,540,020 (12.04%) intergenic = 9,709,301 (12.25%) overlapping exon = 3,525,885 (4.45%) >>>>>>> Transcript coverage profile 5' bias = 0.36 3' bias = 0.27 5'-3' bias = 1.69 >>>>>>> Junction analysis reads at junctions = 19,307,242 ACCT : 5.15% AGGT : 4.63% TCCT : 3.86% ATCT : 3.72% AGGA : 3.39% GCCT : 3.12% CCCT : 2.71% AGCT : 2.55% TTCT : 2.37% AGGC : 2.31% AGAT : 2.07%