RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354119.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) = 56,239,703 / 56,178,094 read pairs aligned = 56,171,379 total alignments = 119,432,590 secondary alignments = 7,014,793 non-unique alignments = 11,549,460 aligned to genes = 91,479,087 ambiguous alignments = 293,944 no feature assigned = 15,503,741 not aligned = 8,841,247 >>>>>>> Reads genomic origin exonic = 91,479,087 (85.51%) intronic = 10,161,947 (9.5%) intergenic = 5,341,794 (4.99%) overlapping exon = 3,834,238 (3.58%) >>>>>>> Transcript coverage profile 5' bias = 0.32 3' bias = 0.17 5'-3' bias = 1.82 >>>>>>> Junction analysis reads at junctions = 26,477,875 ACCT : 5.49% AGGT : 4.81% ATCT : 3.84% AGGA : 3.59% TCCT : 3.38% GCCT : 3.31% AGCT : 2.63% CCCT : 2.56% AGGC : 2.43% AGAT : 2.3% TTCT : 2.24%