RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354094.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) = 49,414,447 / 49,365,990 read pairs aligned = 49,357,278 total alignments = 105,863,399 secondary alignments = 7,082,962 non-unique alignments = 11,549,153 aligned to genes = 83,589,758 ambiguous alignments = 294,154 no feature assigned = 9,814,887 not aligned = 3,301,757 >>>>>>> Reads genomic origin exonic = 83,589,758 (89.49%) intronic = 6,367,889 (6.82%) intergenic = 3,446,998 (3.69%) overlapping exon = 3,446,152 (3.69%) >>>>>>> Transcript coverage profile 5' bias = 0.34 3' bias = 0.23 5'-3' bias = 1.82 >>>>>>> Junction analysis reads at junctions = 27,428,961 ACCT : 5.16% AGGT : 4.61% TCCT : 3.89% ATCT : 3.85% AGGA : 3.36% GCCT : 3.1% CCCT : 2.62% AGCT : 2.61% AGGC : 2.27% TTCT : 2.13% AGAT : 1.97%