RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354143.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) = 42,420,283 / 42,408,075 read pairs aligned = 42,402,310 total alignments = 90,313,194 secondary alignments = 5,484,836 non-unique alignments = 8,866,595 aligned to genes = 71,504,395 ambiguous alignments = 229,608 no feature assigned = 9,238,353 not aligned = 1,906,390 >>>>>>> Reads genomic origin exonic = 71,504,395 (88.56%) intronic = 6,590,273 (8.16%) intergenic = 2,648,080 (3.28%) overlapping exon = 3,031,823 (3.75%) >>>>>>> Transcript coverage profile 5' bias = 0.31 3' bias = 0.17 5'-3' bias = 2.21 >>>>>>> Junction analysis reads at junctions = 24,151,636 ACCT : 5.47% AGGT : 4.69% ATCT : 3.79% TCCT : 3.61% AGGA : 3.5% GCCT : 3.16% AGCT : 2.59% AGGC : 2.34% CCCT : 2.31% AGAT : 2.08% TTCT : 2.04%