RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354139.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) = 45,552,438 / 45,501,949 read pairs aligned = 45,484,368 total alignments = 100,178,578 secondary alignments = 9,124,191 non-unique alignments = 12,406,841 aligned to genes = 75,484,425 ambiguous alignments = 258,981 no feature assigned = 10,003,424 not aligned = 2,756,487 >>>>>>> Reads genomic origin exonic = 75,484,425 (88.3%) intronic = 6,365,459 (7.45%) intergenic = 3,637,965 (4.26%) overlapping exon = 3,619,864 (4.23%) >>>>>>> Transcript coverage profile 5' bias = 0.52 3' bias = 0.22 5'-3' bias = 1.98 >>>>>>> Junction analysis reads at junctions = 23,174,917 ACCT : 5.1% AGGT : 4.84% ATCT : 3.59% TCCT : 3.49% AGGA : 3.42% GCCT : 3.31% CCCT : 2.87% AGCT : 2.76% AGGC : 2.52% TTCT : 2.25% AGAT : 2.11%