RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354158.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) = 38,040,597 / 38,020,033 read pairs aligned = 38,017,133 total alignments = 80,835,963 secondary alignments = 4,775,333 non-unique alignments = 8,054,755 aligned to genes = 63,604,908 ambiguous alignments = 213,872 no feature assigned = 8,703,730 not aligned = 3,390,404 >>>>>>> Reads genomic origin exonic = 63,604,908 (87.96%) intronic = 6,062,516 (8.38%) intergenic = 2,641,214 (3.65%) overlapping exon = 2,260,038 (3.13%) >>>>>>> Transcript coverage profile 5' bias = 0.37 3' bias = 0.17 5'-3' bias = 1.97 >>>>>>> Junction analysis reads at junctions = 21,012,666 ACCT : 5.62% AGGT : 4.67% ATCT : 3.63% AGGA : 3.55% TCCT : 3.42% GCCT : 3.39% AGCT : 2.74% AGGC : 2.38% CCCT : 2.36% AGAT : 2.29% TTCT : 2.16%