RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354413.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) = 37,672,066 / 37,645,130 read pairs aligned = 37,639,967 total alignments = 81,221,889 secondary alignments = 5,904,693 non-unique alignments = 9,958,286 aligned to genes = 64,597,511 ambiguous alignments = 252,937 no feature assigned = 5,993,999 not aligned = 2,696,946 >>>>>>> Reads genomic origin exonic = 64,597,511 (91.51%) intronic = 3,258,735 (4.62%) intergenic = 2,735,264 (3.87%) overlapping exon = 2,419,799 (3.43%) >>>>>>> Transcript coverage profile 5' bias = 0.18 3' bias = 0.2 5'-3' bias = 1.8 >>>>>>> Junction analysis reads at junctions = 19,443,398 ACCT : 5.58% TCCT : 4.75% ATCT : 4.56% AGGT : 4.38% GCCT : 3.36% AGGA : 2.96% CCCT : 2.93% TTCT : 2.27% AGGC : 2.23% AGCT : 2.18% TCCC : 2.13%