RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354136.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) = 42,863,891 / 42,823,200 read pairs aligned = 42,817,518 total alignments = 90,759,587 secondary alignments = 5,072,496 non-unique alignments = 8,584,494 aligned to genes = 73,206,486 ambiguous alignments = 257,821 no feature assigned = 8,427,612 not aligned = 8,308,007 >>>>>>> Reads genomic origin exonic = 73,206,486 (89.68%) intronic = 4,991,353 (6.11%) intergenic = 3,436,259 (4.21%) overlapping exon = 2,800,341 (3.43%) >>>>>>> Transcript coverage profile 5' bias = 0.3 3' bias = 0.17 5'-3' bias = 1.93 >>>>>>> Junction analysis reads at junctions = 24,213,419 ACCT : 5.43% AGGT : 4.63% ATCT : 3.65% TCCT : 3.48% AGGA : 3.42% GCCT : 3.36% AGCT : 2.67% AGGC : 2.47% CCCT : 2.34% AGAT : 2.15% TTCT : 2.12%