RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354393.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) = 126,093,945 / 125,926,247 read pairs aligned = 125,914,605 total alignments = 270,928,955 secondary alignments = 18,908,763 non-unique alignments = 30,390,501 aligned to genes = 215,128,352 ambiguous alignments = 967,544 no feature assigned = 22,773,118 not aligned = 11,107,986 >>>>>>> Reads genomic origin exonic = 215,128,352 (90.43%) intronic = 15,319,157 (6.44%) intergenic = 7,453,961 (3.13%) overlapping exon = 8,993,078 (3.78%) >>>>>>> Transcript coverage profile 5' bias = 0.3 3' bias = 0.22 5'-3' bias = 1.71 >>>>>>> Junction analysis reads at junctions = 78,567,120 ACCT : 5.38% AGGT : 4.39% ATCT : 4.1% TCCT : 3.98% GCCT : 3.51% AGGA : 3.12% CCCT : 2.75% TTCT : 2.51% AGCT : 2.48% AGGC : 2.29% AGAT : 1.9%