RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354161.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) = 34,191,465 / 34,171,478 read pairs aligned = 34,167,863 total alignments = 72,666,331 secondary alignments = 4,303,388 non-unique alignments = 6,893,391 aligned to genes = 58,001,234 ambiguous alignments = 209,823 no feature assigned = 7,149,163 not aligned = 1,784,577 >>>>>>> Reads genomic origin exonic = 58,001,234 (89.03%) intronic = 5,085,272 (7.81%) intergenic = 2,063,891 (3.17%) overlapping exon = 2,083,076 (3.2%) >>>>>>> Transcript coverage profile 5' bias = 0.35 3' bias = 0.22 5'-3' bias = 1.75 >>>>>>> Junction analysis reads at junctions = 19,090,308 ACCT : 5.32% AGGT : 4.56% ATCT : 3.61% TCCT : 3.55% AGGA : 3.37% GCCT : 3.36% AGCT : 2.68% CCCT : 2.44% TTCT : 2.34% AGGC : 2.32% AGAT : 2.09%