RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354402.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) = 34,159,486 / 34,105,407 read pairs aligned = 34,101,640 total alignments = 73,367,407 secondary alignments = 5,102,514 non-unique alignments = 8,573,792 aligned to genes = 57,701,489 ambiguous alignments = 198,929 no feature assigned = 6,559,532 not aligned = 4,379,369 >>>>>>> Reads genomic origin exonic = 57,701,489 (89.79%) intronic = 3,921,545 (6.1%) intergenic = 2,637,987 (4.11%) overlapping exon = 2,060,095 (3.21%) >>>>>>> Transcript coverage profile 5' bias = 0.38 3' bias = 0.22 5'-3' bias = 1.9 >>>>>>> Junction analysis reads at junctions = 17,746,189 ACCT : 5.31% AGGT : 4.61% ATCT : 3.8% TCCT : 3.48% AGGA : 3.38% GCCT : 3.24% AGCT : 2.61% CCCT : 2.44% TTCT : 2.42% AGGC : 2.37% AGAT : 2.09%