RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354140.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) = 103,680,630 / 103,557,076 read pairs aligned = 103,538,379 total alignments = 221,428,415 secondary alignments = 14,190,709 non-unique alignments = 23,931,912 aligned to genes = 171,102,614 ambiguous alignments = 650,177 no feature assigned = 24,801,147 not aligned = 6,840,020 >>>>>>> Reads genomic origin exonic = 171,102,614 (87.34%) intronic = 16,858,786 (8.61%) intergenic = 7,942,361 (4.05%) overlapping exon = 7,689,064 (3.92%) >>>>>>> Transcript coverage profile 5' bias = 0.45 3' bias = 0.22 5'-3' bias = 1.81 >>>>>>> Junction analysis reads at junctions = 56,212,798 ACCT : 5.17% AGGT : 4.88% AGGA : 3.6% TCCT : 3.47% ATCT : 3.43% GCCT : 3.01% AGCT : 2.76% CCCT : 2.62% AGGC : 2.54% AGAT : 2.32% TTCT : 2.23%