RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354369.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) = 33,611,551 / 33,586,772 read pairs aligned = 33,581,637 total alignments = 72,896,790 secondary alignments = 5,698,467 non-unique alignments = 8,773,058 aligned to genes = 53,968,390 ambiguous alignments = 219,442 no feature assigned = 9,283,782 not aligned = 3,771,281 >>>>>>> Reads genomic origin exonic = 53,968,390 (85.32%) intronic = 7,108,273 (11.24%) intergenic = 2,175,509 (3.44%) overlapping exon = 1,840,045 (2.91%) >>>>>>> Transcript coverage profile 5' bias = 0.37 3' bias = 0.22 5'-3' bias = 1.89 >>>>>>> Junction analysis reads at junctions = 19,284,399 ACCT : 5.48% AGGT : 4.5% TCCT : 3.6% ATCT : 3.52% AGGA : 3.48% GCCT : 3.29% AGCT : 2.71% CCCT : 2.42% AGGC : 2.27% AGAT : 2.25% TTCT : 2.18%