RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354304.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) = 36,151,874 / 36,130,923 read pairs aligned = 36,126,973 total alignments = 76,902,887 secondary alignments = 4,620,090 non-unique alignments = 7,351,077 aligned to genes = 60,816,070 ambiguous alignments = 238,108 no feature assigned = 8,062,820 not aligned = 3,374,095 >>>>>>> Reads genomic origin exonic = 60,816,070 (88.29%) intronic = 5,868,829 (8.52%) intergenic = 2,193,991 (3.19%) overlapping exon = 2,414,822 (3.51%) >>>>>>> Transcript coverage profile 5' bias = 0.29 3' bias = 0.18 5'-3' bias = 1.9 >>>>>>> Junction analysis reads at junctions = 20,162,559 ACCT : 5.47% AGGT : 4.7% ATCT : 3.75% AGGA : 3.45% TCCT : 3.41% GCCT : 3.14% AGCT : 2.62% CCCT : 2.4% AGGC : 2.33% TTCT : 2.16% AGAT : 2.11%