RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354147.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) = 38,166,533 / 38,136,365 read pairs aligned = 38,131,931 total alignments = 81,076,961 secondary alignments = 4,774,063 non-unique alignments = 7,892,544 aligned to genes = 60,627,608 ambiguous alignments = 260,879 no feature assigned = 11,921,810 not aligned = 5,729,070 >>>>>>> Reads genomic origin exonic = 60,627,608 (83.57%) intronic = 7,234,347 (9.97%) intergenic = 4,687,463 (6.46%) overlapping exon = 2,826,480 (3.9%) >>>>>>> Transcript coverage profile 5' bias = 0.45 3' bias = 0.31 5'-3' bias = 1.73 >>>>>>> Junction analysis reads at junctions = 21,016,047 ACCT : 5.14% AGGT : 4.7% TCCT : 3.71% ATCT : 3.5% AGGA : 3.46% GCCT : 3.39% CCCT : 2.73% AGCT : 2.69% AGGC : 2.48% AGAT : 2.14% TTCT : 2.11%