RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354349.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) = 45,068,723 / 44,952,878 read pairs aligned = 44,934,915 total alignments = 96,660,658 secondary alignments = 6,639,057 non-unique alignments = 10,940,999 aligned to genes = 72,602,270 ambiguous alignments = 284,043 no feature assigned = 12,589,307 not aligned = 7,240,043 >>>>>>> Reads genomic origin exonic = 72,602,270 (85.22%) intronic = 10,527,468 (12.36%) intergenic = 2,061,839 (2.42%) overlapping exon = 3,610,128 (4.24%) >>>>>>> Transcript coverage profile 5' bias = 0.34 3' bias = 0.17 5'-3' bias = 1.83 >>>>>>> Junction analysis reads at junctions = 28,092,943 ACCT : 5.8% AGGT : 4.78% TCCT : 3.76% AGGA : 3.76% ATCT : 3.45% AGCT : 2.68% AGAT : 2.42% TTCT : 2.28% GCCT : 2.26% AGGC : 2.24% CCCT : 2.22%