RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354356.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) = 35,152,075 / 35,130,677 read pairs aligned = 35,127,068 total alignments = 74,951,306 secondary alignments = 4,668,554 non-unique alignments = 7,834,381 aligned to genes = 58,824,585 ambiguous alignments = 202,820 no feature assigned = 7,820,388 not aligned = 4,177,960 >>>>>>> Reads genomic origin exonic = 58,824,585 (88.27%) intronic = 5,233,329 (7.85%) intergenic = 2,587,059 (3.88%) overlapping exon = 2,129,191 (3.19%) >>>>>>> Transcript coverage profile 5' bias = 0.33 3' bias = 0.15 5'-3' bias = 2.42 >>>>>>> Junction analysis reads at junctions = 17,972,173 ACCT : 5.33% AGGT : 4.7% ATCT : 3.62% AGGA : 3.6% TCCT : 3.51% GCCT : 3.07% AGCT : 2.65% AGGC : 2.34% CCCT : 2.28% AGAT : 2.27% TTCT : 2.11%