RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354057.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) = 37,022,810 / 36,993,632 read pairs aligned = 36,990,630 total alignments = 79,346,136 secondary alignments = 5,329,694 non-unique alignments = 8,852,599 aligned to genes = 61,068,937 ambiguous alignments = 249,758 no feature assigned = 8,806,684 not aligned = 2,353,108 >>>>>>> Reads genomic origin exonic = 61,068,937 (87.4%) intronic = 6,477,740 (9.27%) intergenic = 2,328,944 (3.33%) overlapping exon = 2,471,330 (3.54%) >>>>>>> Transcript coverage profile 5' bias = 0.39 3' bias = 0.24 5'-3' bias = 1.73 >>>>>>> Junction analysis reads at junctions = 22,097,158 ACCT : 5.34% AGGT : 4.61% ATCT : 3.45% TCCT : 3.45% GCCT : 3.44% AGGA : 3.4% AGCT : 2.77% CCCT : 2.47% AGGC : 2.37% AGAT : 2.2% TTCT : 2.19%