RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354169.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) = 35,480,002 / 35,455,077 read pairs aligned = 35,451,305 total alignments = 75,229,006 secondary alignments = 4,293,927 non-unique alignments = 7,234,305 aligned to genes = 58,191,198 ambiguous alignments = 190,978 no feature assigned = 9,319,653 not aligned = 7,300,127 >>>>>>> Reads genomic origin exonic = 58,191,198 (86.2%) intronic = 5,833,759 (8.64%) intergenic = 3,485,894 (5.16%) overlapping exon = 2,390,007 (3.54%) >>>>>>> Transcript coverage profile 5' bias = 0.26 3' bias = 0.14 5'-3' bias = 2.33 >>>>>>> Junction analysis reads at junctions = 16,390,684 ACCT : 5.48% AGGT : 4.73% ATCT : 3.65% AGGA : 3.59% TCCT : 3.42% GCCT : 3.09% AGCT : 2.75% AGGC : 2.38% AGAT : 2.34% CCCT : 2.31% TTCT : 2.22%