RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354181.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) = 50,691,717 / 50,649,246 read pairs aligned = 50,636,319 total alignments = 109,071,547 secondary alignments = 7,730,584 non-unique alignments = 12,188,282 aligned to genes = 86,655,448 ambiguous alignments = 307,759 no feature assigned = 9,035,260 not aligned = 6,529,587 >>>>>>> Reads genomic origin exonic = 86,655,448 (90.56%) intronic = 5,169,163 (5.4%) intergenic = 3,866,097 (4.04%) overlapping exon = 3,564,266 (3.72%) >>>>>>> Transcript coverage profile 5' bias = 0.25 3' bias = 0.21 5'-3' bias = 1.87 >>>>>>> Junction analysis reads at junctions = 24,993,748 ACCT : 5.28% AGGT : 4.7% ATCT : 4.14% TCCT : 4.07% AGGA : 3.29% GCCT : 3.17% CCCT : 2.83% AGCT : 2.4% AGGC : 2.23% TTCT : 2.22% AGAA : 1.98%