RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354366.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) = 43,915,520 / 43,885,363 read pairs aligned = 43,877,800 total alignments = 94,676,713 secondary alignments = 6,875,830 non-unique alignments = 11,024,144 aligned to genes = 75,194,631 ambiguous alignments = 324,076 no feature assigned = 7,471,814 not aligned = 2,364,129 >>>>>>> Reads genomic origin exonic = 75,194,631 (90.96%) intronic = 4,572,447 (5.53%) intergenic = 2,899,367 (3.51%) overlapping exon = 3,373,207 (4.08%) >>>>>>> Transcript coverage profile 5' bias = 0.21 3' bias = 0.2 5'-3' bias = 2.01 >>>>>>> Junction analysis reads at junctions = 27,026,674 ACCT : 5.26% ATCT : 4.95% TCCT : 4.82% AGGT : 4.15% GCCT : 3.37% CCCT : 3.09% AGGA : 2.93% TTCT : 2.28% AGCT : 2.21% AGGC : 2.06% TCCC : 2.05%