RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354210.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) = 44,890,175 / 44,872,580 read pairs aligned = 44,865,272 total alignments = 97,973,167 secondary alignments = 8,210,412 non-unique alignments = 12,356,701 aligned to genes = 76,578,948 ambiguous alignments = 282,933 no feature assigned = 7,697,755 not aligned = 3,036,901 >>>>>>> Reads genomic origin exonic = 76,578,948 (90.87%) intronic = 4,940,927 (5.86%) intergenic = 2,756,828 (3.27%) overlapping exon = 3,620,386 (4.3%) >>>>>>> Transcript coverage profile 5' bias = 0.15 3' bias = 0.16 5'-3' bias = 2.15 >>>>>>> Junction analysis reads at junctions = 31,604,985 ACCT : 5.28% TCCT : 4.57% AGGT : 4.48% ATCT : 4.35% AGGA : 3.02% CCCT : 2.7% GCCT : 2.45% AGGC : 2.23% AGCT : 2% TTCT : 1.94% AACT : 1.83%