RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354088.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) = 38,524,073 / 38,489,984 read pairs aligned = 38,453,304 total alignments = 90,347,357 secondary alignments = 13,333,300 non-unique alignments = 18,998,700 aligned to genes = 52,448,124 ambiguous alignments = 224,684 no feature assigned = 16,104,246 not aligned = 4,378,773 >>>>>>> Reads genomic origin exonic = 52,448,124 (76.51%) intronic = 7,240,639 (10.56%) intergenic = 8,863,607 (12.93%) overlapping exon = 4,240,578 (6.19%) >>>>>>> Transcript coverage profile 5' bias = 0.09 3' bias = 0.11 5'-3' bias = 1.92 >>>>>>> Junction analysis reads at junctions = 18,228,230 TCCT : 8.44% ATCT : 6.04% ACCT : 4.78% CCCT : 4.3% AGGT : 3.34% GTCT : 3.28% TCCG : 3.19% AGGA : 2.76% TTCT : 2.42% AGAC : 2.09% GCCT : 1.93%