RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354392.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) = 44,727,881 / 44,703,078 read pairs aligned = 44,696,610 total alignments = 95,141,445 secondary alignments = 5,710,486 non-unique alignments = 9,154,232 aligned to genes = 73,332,745 ambiguous alignments = 284,453 no feature assigned = 11,882,841 not aligned = 2,412,497 >>>>>>> Reads genomic origin exonic = 73,332,745 (86.06%) intronic = 9,145,377 (10.73%) intergenic = 2,737,464 (3.21%) overlapping exon = 3,176,893 (3.73%) >>>>>>> Transcript coverage profile 5' bias = 0.32 3' bias = 0.21 5'-3' bias = 1.71 >>>>>>> Junction analysis reads at junctions = 25,989,169 ACCT : 5.17% AGGT : 4.69% AGGA : 3.56% ATCT : 3.5% TCCT : 3.38% GCCT : 2.99% AGCT : 2.82% AGGC : 2.33% AGAT : 2.32% CCCT : 2.31% TTCT : 2.26%