RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354244.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) = 18,291,837 / 18,281,733 read pairs aligned = 18,280,040 total alignments = 38,943,229 secondary alignments = 2,369,659 non-unique alignments = 3,890,389 aligned to genes = 30,311,160 ambiguous alignments = 110,610 no feature assigned = 4,449,287 not aligned = 1,687,854 >>>>>>> Reads genomic origin exonic = 30,311,160 (87.2%) intronic = 3,104,436 (8.93%) intergenic = 1,344,851 (3.87%) overlapping exon = 1,164,664 (3.35%) >>>>>>> Transcript coverage profile 5' bias = 0.38 3' bias = 0.19 5'-3' bias = 2.2 >>>>>>> Junction analysis reads at junctions = 10,310,923 ACCT : 5.27% AGGT : 4.7% TCCT : 3.61% ATCT : 3.56% AGGA : 3.55% GCCT : 2.94% AGCT : 2.7% CCCT : 2.45% AGGC : 2.41% AGAT : 2.23% TTCT : 2.13%