RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354261.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) = 46,467,889 / 46,415,739 read pairs aligned = 46,391,186 total alignments = 99,528,063 secondary alignments = 6,644,435 non-unique alignments = 10,313,707 aligned to genes = 78,071,355 ambiguous alignments = 385,191 no feature assigned = 9,970,882 not aligned = 2,447,362 >>>>>>> Reads genomic origin exonic = 78,071,355 (88.67%) intronic = 6,463,156 (7.34%) intergenic = 3,507,726 (3.98%) overlapping exon = 4,719,965 (5.36%) >>>>>>> Transcript coverage profile 5' bias = 0.25 3' bias = 0.19 5'-3' bias = 1.95 >>>>>>> Junction analysis reads at junctions = 28,142,784 ACCT : 5.52% TCCT : 5.13% ATCT : 4.53% AGGT : 4.16% CCCT : 3.29% GCCT : 3.18% AGGA : 2.91% TTCT : 2.36% AGGC : 2.22% GTCT : 2.13% AGCT : 2.08%