RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354271.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) = 41,483,626 / 41,451,093 read pairs aligned = 41,447,561 total alignments = 87,736,408 secondary alignments = 4,801,689 non-unique alignments = 8,092,240 aligned to genes = 71,296,545 ambiguous alignments = 219,525 no feature assigned = 7,799,261 not aligned = 2,855,393 >>>>>>> Reads genomic origin exonic = 71,296,545 (90.14%) intronic = 4,462,095 (5.64%) intergenic = 3,337,166 (4.22%) overlapping exon = 2,717,662 (3.44%) >>>>>>> Transcript coverage profile 5' bias = 0.48 3' bias = 0.17 5'-3' bias = 2.28 >>>>>>> Junction analysis reads at junctions = 23,632,681 ACCT : 5.4% AGGT : 4.67% AGGA : 3.6% ATCT : 3.52% TCCT : 3.4% GCCT : 3.11% AGCT : 2.75% AGGC : 2.38% AGAT : 2.32% CCCT : 2.28% TTCT : 2.12%