RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354350.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) = 36,264,754 / 36,238,511 read pairs aligned = 36,233,555 total alignments = 77,738,377 secondary alignments = 5,235,112 non-unique alignments = 8,432,839 aligned to genes = 59,945,597 ambiguous alignments = 202,316 no feature assigned = 8,637,649 not aligned = 3,286,887 >>>>>>> Reads genomic origin exonic = 59,945,597 (87.41%) intronic = 6,045,105 (8.81%) intergenic = 2,592,544 (3.78%) overlapping exon = 2,185,336 (3.19%) >>>>>>> Transcript coverage profile 5' bias = 0.43 3' bias = 0.24 5'-3' bias = 1.86 >>>>>>> Junction analysis reads at junctions = 18,095,049 ACCT : 5.31% AGGT : 4.65% ATCT : 3.6% AGGA : 3.46% GCCT : 3.42% TCCT : 3.38% AGCT : 2.72% CCCT : 2.52% AGGC : 2.36% TTCT : 2.32% AGAT : 2.21%