RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354165.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) = 46,366,482 / 46,339,236 read pairs aligned = 46,334,477 total alignments = 98,372,911 secondary alignments = 5,667,193 non-unique alignments = 9,641,837 aligned to genes = 75,389,476 ambiguous alignments = 195,146 no feature assigned = 12,769,900 not aligned = 5,059,886 >>>>>>> Reads genomic origin exonic = 75,389,476 (85.51%) intronic = 7,132,760 (8.09%) intergenic = 5,637,140 (6.39%) overlapping exon = 3,385,638 (3.84%) >>>>>>> Transcript coverage profile 5' bias = 0.25 3' bias = 0.21 5'-3' bias = 2.01 >>>>>>> Junction analysis reads at junctions = 16,440,295 ACCT : 5.14% AGGT : 4.7% ATCT : 3.99% TCCT : 3.71% AGGA : 3.65% GCCT : 2.91% CCCT : 2.63% AGCT : 2.54% AGGC : 2.36% TTCT : 2.24% AGAT : 2.23%