RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354170.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) = 24,267,084 / 24,253,501 read pairs aligned = 24,249,879 total alignments = 52,226,663 secondary alignments = 3,706,078 non-unique alignments = 6,342,544 aligned to genes = 39,523,490 ambiguous alignments = 98,501 no feature assigned = 6,036,550 not aligned = 1,365,875 >>>>>>> Reads genomic origin exonic = 39,523,490 (86.75%) intronic = 3,354,052 (7.36%) intergenic = 2,682,498 (5.89%) overlapping exon = 1,777,156 (3.9%) >>>>>>> Transcript coverage profile 5' bias = 0.3 3' bias = 0.13 5'-3' bias = 2.35 >>>>>>> Junction analysis reads at junctions = 8,078,529 ACCT : 5.25% AGGT : 4.62% ATCT : 3.64% AGGA : 3.51% TCCT : 3.4% GCCT : 3.26% AGCT : 2.64% TTCT : 2.39% CCCT : 2.31% AGGC : 2.24% AGAT : 2.19%