RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354066.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) = 40,023,127 / 39,999,985 read pairs aligned = 39,997,496 total alignments = 87,454,278 secondary alignments = 7,431,166 non-unique alignments = 12,993,793 aligned to genes = 66,569,187 ambiguous alignments = 176,801 no feature assigned = 7,340,379 not aligned = 1,643,388 >>>>>>> Reads genomic origin exonic = 66,569,187 (90.07%) intronic = 4,089,167 (5.53%) intergenic = 3,251,212 (4.4%) overlapping exon = 2,082,097 (2.82%) >>>>>>> Transcript coverage profile 5' bias = 0.15 3' bias = 0.14 5'-3' bias = 1.95 >>>>>>> Junction analysis reads at junctions = 14,228,902 ACCT : 5.14% ATCT : 4.69% AGGT : 4.24% TCCT : 3.8% GCCT : 3.39% AGGA : 3.27% CCCT : 2.91% TTCT : 2.48% AGCT : 2.25% AGGC : 2.12% TCCC : 1.93%