RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354194.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) = 35,487,047 / 35,466,496 read pairs aligned = 35,463,211 total alignments = 75,429,033 secondary alignments = 4,475,490 non-unique alignments = 7,513,282 aligned to genes = 60,009,512 ambiguous alignments = 196,428 no feature assigned = 7,390,473 not aligned = 4,749,257 >>>>>>> Reads genomic origin exonic = 60,009,512 (89.03%) intronic = 4,372,054 (6.49%) intergenic = 3,018,419 (4.48%) overlapping exon = 2,134,930 (3.17%) >>>>>>> Transcript coverage profile 5' bias = 0.32 3' bias = 0.18 5'-3' bias = 2.28 >>>>>>> Junction analysis reads at junctions = 17,821,940 ACCT : 5.44% AGGT : 4.81% AGGA : 3.71% ATCT : 3.66% TCCT : 3.5% GCCT : 2.98% AGCT : 2.71% AGGC : 2.41% CCCT : 2.37% AGAT : 2.35% TTCT : 2.09%