RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354307.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) = 47,187,521 / 47,142,426 read pairs aligned = 47,137,633 total alignments = 101,333,103 secondary alignments = 7,003,156 non-unique alignments = 10,355,728 aligned to genes = 79,004,146 ambiguous alignments = 276,424 no feature assigned = 10,498,987 not aligned = 9,256,473 >>>>>>> Reads genomic origin exonic = 79,004,146 (88.27%) intronic = 5,265,352 (5.88%) intergenic = 5,233,635 (5.85%) overlapping exon = 3,086,654 (3.45%) >>>>>>> Transcript coverage profile 5' bias = 0.56 3' bias = 0.28 5'-3' bias = 1.81 >>>>>>> Junction analysis reads at junctions = 28,092,846 ACCT : 5.11% AGGT : 4.73% ATCT : 3.53% AGGA : 3.48% TCCT : 3.45% GCCT : 3.31% AGCT : 2.86% CCCT : 2.69% AGGC : 2.41% TTCT : 2.22% AGAT : 2.14%