RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354364.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) = 34,740,486 / 34,720,478 read pairs aligned = 34,701,275 total alignments = 75,087,935 secondary alignments = 5,626,971 non-unique alignments = 9,207,791 aligned to genes = 58,857,877 ambiguous alignments = 257,335 no feature assigned = 6,244,729 not aligned = 1,446,782 >>>>>>> Reads genomic origin exonic = 58,857,877 (90.41%) intronic = 3,616,236 (5.55%) intergenic = 2,628,493 (4.04%) overlapping exon = 2,732,252 (4.2%) >>>>>>> Transcript coverage profile 5' bias = 0.37 3' bias = 0.26 5'-3' bias = 1.95 >>>>>>> Junction analysis reads at junctions = 18,475,952 ACCT : 5.14% TCCT : 4.6% AGGT : 4.44% ATCT : 4.27% CCCT : 3.27% AGGA : 3.19% GCCT : 3.17% AGCT : 2.4% AGGC : 2.27% TTCT : 2.11% GTCT : 1.76%