RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354056.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) = 34,899,189 / 34,876,402 read pairs aligned = 34,873,718 total alignments = 74,435,635 secondary alignments = 4,660,044 non-unique alignments = 7,611,070 aligned to genes = 58,528,694 ambiguous alignments = 212,822 no feature assigned = 7,717,364 not aligned = 2,114,851 >>>>>>> Reads genomic origin exonic = 58,528,694 (88.35%) intronic = 5,518,300 (8.33%) intergenic = 2,199,064 (3.32%) overlapping exon = 2,266,523 (3.42%) >>>>>>> Transcript coverage profile 5' bias = 0.37 3' bias = 0.22 5'-3' bias = 1.81 >>>>>>> Junction analysis reads at junctions = 20,776,077 ACCT : 5.35% AGGT : 4.53% ATCT : 3.77% TCCT : 3.6% AGGA : 3.35% GCCT : 3.34% AGCT : 2.68% CCCT : 2.42% AGGC : 2.36% TTCT : 2.15% AGAT : 2.09%