RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354273.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) = 56,403,401 / 56,389,292 read pairs aligned = 56,386,297 total alignments = 122,383,193 secondary alignments = 9,590,500 non-unique alignments = 15,218,940 aligned to genes = 80,785,428 ambiguous alignments = 279,689 no feature assigned = 25,048,532 not aligned = 1,266,567 >>>>>>> Reads genomic origin exonic = 80,785,428 (76.33%) intronic = 11,892,032 (11.24%) intergenic = 13,156,500 (12.43%) overlapping exon = 3,434,460 (3.25%) >>>>>>> Transcript coverage profile 5' bias = 0.5 3' bias = 0.22 5'-3' bias = 1.88 >>>>>>> Junction analysis reads at junctions = 31,615,124 ACCT : 4.79% AGGT : 4.49% ATCT : 3.67% TCCT : 3.58% AGGA : 3.39% GCCT : 3.33% CCCT : 2.71% AGCT : 2.6% TTCT : 2.44% AGGC : 2.27% AGAT : 2%