RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354207.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) = 42,232,833 / 42,208,619 read pairs aligned = 42,200,447 total alignments = 89,788,179 secondary alignments = 5,346,727 non-unique alignments = 8,264,363 aligned to genes = 69,071,347 ambiguous alignments = 236,738 no feature assigned = 11,547,647 not aligned = 2,097,226 >>>>>>> Reads genomic origin exonic = 69,071,347 (85.68%) intronic = 8,224,162 (10.2%) intergenic = 3,323,485 (4.12%) overlapping exon = 3,245,592 (4.03%) >>>>>>> Transcript coverage profile 5' bias = 0.42 3' bias = 0.17 5'-3' bias = 2.07 >>>>>>> Junction analysis reads at junctions = 22,830,658 ACCT : 5.41% AGGT : 4.78% AGGA : 3.57% ATCT : 3.53% GCCT : 3.32% TCCT : 3.29% AGCT : 2.7% AGGC : 2.42% CCCT : 2.33% AGAT : 2.29% TTCT : 2.13%