Input data and parameters 

Input

Analysis date: Mon Oct 30 09:51:12 GMT 2023
BAM file: SRX7354064.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): 58,435,666 / 58,324,439
Number of aligned pairs (without duplicates): 58,315,493
Total number of alignments: 125,651,064
Number of secondary alignments: 8,890,959
Number of non-unique alignments: 13,939,944
Aligned to genes: 90,511,023
Ambiguous alignments: 337,133
No feature assigned: 19,838,797
Missing chromosome in annotation: 1,024,167
Not aligned: 16,168,087

Reads genomic origin

Exonic: 90,511,023 / 82.02%
Intronic: 12,266,614 / 11.12%
Intergenic: 7,572,183 / 6.86%
Intronic/intergenic overlapping exon: 3,985,199 / 3.61%

Transcript coverage profile

5' bias: 0.41
3' bias: 0.32
5'-3' bias: 1.72

Junction analysis

Reads at junctions: 35,141,538
ACCT 5.07%
AGGT 4.6%
TCCT 3.96%
ATCT 3.74%
GCCT 3.45%
AGGA 3.23%
CCCT 2.77%
AGCT 2.69%
AGGC 2.51%
TTCT 2.21%
AGAT 1.95%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis