RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354085.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) = 49,369,796 / 49,337,492 read pairs aligned = 49,331,759 total alignments = 105,178,227 secondary alignments = 6,470,939 non-unique alignments = 10,879,826 aligned to genes = 80,902,865 ambiguous alignments = 270,739 no feature assigned = 12,700,796 not aligned = 7,091,938 >>>>>>> Reads genomic origin exonic = 80,902,865 (86.43%) intronic = 8,029,222 (8.58%) intergenic = 4,671,574 (4.99%) overlapping exon = 3,295,364 (3.52%) >>>>>>> Transcript coverage profile 5' bias = 0.28 3' bias = 0.18 5'-3' bias = 1.75 >>>>>>> Junction analysis reads at junctions = 23,883,255 ACCT : 5.38% AGGT : 4.77% AGGA : 3.58% ATCT : 3.53% TCCT : 3.39% GCCT : 3.22% AGCT : 2.75% AGGC : 2.43% CCCT : 2.36% AGAT : 2.34% TTCT : 2.25%