RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354292.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) = 32,513,660 / 32,502,871 read pairs aligned = 32,500,359 total alignments = 68,830,076 secondary alignments = 3,813,545 non-unique alignments = 5,982,218 aligned to genes = 54,881,193 ambiguous alignments = 190,290 no feature assigned = 7,350,482 not aligned = 911,743 >>>>>>> Reads genomic origin exonic = 54,881,193 (88.19%) intronic = 5,056,174 (8.12%) intergenic = 2,294,308 (3.69%) overlapping exon = 2,151,538 (3.46%) >>>>>>> Transcript coverage profile 5' bias = 0.28 3' bias = 0.14 5'-3' bias = 2.23 >>>>>>> Junction analysis reads at junctions = 18,961,980 ACCT : 5.61% AGGT : 4.69% ATCT : 3.65% AGGA : 3.56% TCCT : 3.41% GCCT : 3.13% AGCT : 2.72% AGGC : 2.42% AGAT : 2.29% CCCT : 2.25% TTCT : 2.09%