RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354394.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) = 35,968,400 / 35,877,814 read pairs aligned = 35,830,916 total alignments = 77,017,935 secondary alignments = 5,171,721 non-unique alignments = 8,424,568 aligned to genes = 61,166,382 ambiguous alignments = 215,708 no feature assigned = 6,728,245 not aligned = 6,342,294 >>>>>>> Reads genomic origin exonic = 61,166,382 (90.09%) intronic = 3,571,791 (5.26%) intergenic = 3,156,454 (4.65%) overlapping exon = 2,862,813 (4.22%) >>>>>>> Transcript coverage profile 5' bias = 0.36 3' bias = 0.22 5'-3' bias = 1.92 >>>>>>> Junction analysis reads at junctions = 20,547,149 ACCT : 5.52% TCCT : 4.63% ATCT : 4.32% AGGT : 4.29% GCCT : 3.54% AGGA : 2.89% CCCT : 2.63% AGCT : 2.38% AGGC : 2.24% TTCT : 2.23% TCCC : 2.17%