RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354185.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) = 45,349,643 / 45,314,964 read pairs aligned = 45,305,278 total alignments = 97,083,497 secondary alignments = 6,418,890 non-unique alignments = 10,426,378 aligned to genes = 76,248,076 ambiguous alignments = 285,236 no feature assigned = 9,556,886 not aligned = 4,224,585 >>>>>>> Reads genomic origin exonic = 76,248,076 (88.86%) intronic = 6,508,802 (7.59%) intergenic = 3,048,084 (3.55%) overlapping exon = 3,373,471 (3.93%) >>>>>>> Transcript coverage profile 5' bias = 0.33 3' bias = 0.21 5'-3' bias = 2.04 >>>>>>> Junction analysis reads at junctions = 25,795,808 ACCT : 5.08% AGGT : 4.69% ATCT : 4.19% TCCT : 3.57% GCCT : 3.34% AGGA : 3.32% AGCT : 2.6% CCCT : 2.56% AGGC : 2.34% TTCT : 2.08% AGAT : 1.96%