RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354344.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) = 38,731,464 / 38,697,306 read pairs aligned = 38,693,744 total alignments = 82,525,911 secondary alignments = 5,097,141 non-unique alignments = 8,680,446 aligned to genes = 65,071,975 ambiguous alignments = 240,079 no feature assigned = 8,244,553 not aligned = 3,129,702 >>>>>>> Reads genomic origin exonic = 65,071,975 (88.75%) intronic = 5,229,003 (7.13%) intergenic = 3,015,550 (4.11%) overlapping exon = 2,409,472 (3.29%) >>>>>>> Transcript coverage profile 5' bias = 0.31 3' bias = 0.2 5'-3' bias = 1.85 >>>>>>> Junction analysis reads at junctions = 19,444,197 ACCT : 5.34% AGGT : 4.6% ATCT : 3.68% TCCT : 3.67% AGGA : 3.46% GCCT : 3.34% AGCT : 2.64% CCCT : 2.61% AGGC : 2.44% AGAT : 2.23% TTCT : 2.16%