RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354089.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) = 39,245,384 / 39,207,108 read pairs aligned = 39,202,588 total alignments = 83,230,503 secondary alignments = 4,778,011 non-unique alignments = 8,038,896 aligned to genes = 65,922,604 ambiguous alignments = 206,603 no feature assigned = 8,718,287 not aligned = 8,364,196 >>>>>>> Reads genomic origin exonic = 65,922,604 (88.32%) intronic = 5,360,025 (7.18%) intergenic = 3,358,262 (4.5%) overlapping exon = 2,750,948 (3.69%) >>>>>>> Transcript coverage profile 5' bias = 0.32 3' bias = 0.18 5'-3' bias = 1.99 >>>>>>> Junction analysis reads at junctions = 19,881,417 ACCT : 5.26% AGGT : 4.68% ATCT : 4.07% TCCT : 3.51% AGGA : 3.45% GCCT : 3.22% AGCT : 2.61% CCCT : 2.54% AGGC : 2.34% TTCT : 2.2% AGAT : 2.13%