RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354347.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) = 52,167,326 / 52,125,885 read pairs aligned = 52,113,449 total alignments = 134,902,063 secondary alignments = 30,608,852 non-unique alignments = 25,019,849 aligned to genes = 83,252,552 ambiguous alignments = 381,211 no feature assigned = 11,848,255 not aligned = 6,522,903 >>>>>>> Reads genomic origin exonic = 83,252,552 (87.54%) intronic = 7,746,584 (8.15%) intergenic = 4,101,671 (4.31%) overlapping exon = 3,642,252 (3.83%) >>>>>>> Transcript coverage profile 5' bias = 0.23 3' bias = 0.21 5'-3' bias = 2 >>>>>>> Junction analysis reads at junctions = 28,971,195 ACCT : 5.45% AGGT : 4.47% TCCT : 4.41% ATCT : 4.15% CCCT : 3.25% GCCT : 3.21% AGGA : 3.01% AGGC : 2.38% AGCT : 2.21% TTCT : 2.15% AGAA : 1.74%