Input data and parameters 

Input

Analysis date: Sun Oct 29 01:57:57 GMT 2023
BAM file: SRX7354109.markdup.sorted.bam
Counting algorithm: uniquely-mapped-reads
GTF file: gencode.v44.annotation_genes_collapsed_only_patched_ERCC92.gtf
Number of bases for 5'-3' bias computation: 100
Number of transcripts for 5'-3' bias computation: 1,000
Paired-end sequencing: yes
Protocol: strand-specific-reverse
Sorting performed: yes

Summary 

Reads alignment

Number of mapped reads (left/right): 45,462,120 / 45,413,785
Number of aligned pairs (without duplicates): 45,401,913
Total number of alignments: 96,206,842
Number of secondary alignments: 5,330,937
Number of non-unique alignments: 8,757,011
Aligned to genes: 75,424,820
Ambiguous alignments: 236,025
No feature assigned: 11,338,793
Missing chromosome in annotation: 450,193
Not aligned: 8,587,413

Reads genomic origin

Exonic: 75,424,820 / 86.93%
Intronic: 6,582,804 / 7.59%
Intergenic: 4,755,989 / 5.48%
Intronic/intergenic overlapping exon: 3,386,627 / 3.9%

Transcript coverage profile

5' bias: 0.28
3' bias: 0.16
5'-3' bias: 1.78

Junction analysis

Reads at junctions: 23,191,804
ACCT 5.2%
AGGT 4.69%
ATCT 3.68%
AGGA 3.66%
TCCT 3.33%
GCCT 3.07%
AGCT 2.84%
AGGC 2.37%
CCCT 2.37%
AGAT 2.28%
TTCT 2.21%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis