Input data and parameters 

Input

Analysis date: Mon Oct 30 22:52:03 GMT 2023
BAM file: SRX7354288.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): 52,671,655 / 52,643,361
Number of aligned pairs (without duplicates): 52,631,448
Total number of alignments: 113,282,305
Number of secondary alignments: 7,967,289
Number of non-unique alignments: 12,852,428
Aligned to genes: 91,808,008
Ambiguous alignments: 345,344
No feature assigned: 7,477,225
Missing chromosome in annotation: 799,300
Not aligned: 3,291,346

Reads genomic origin

Exonic: 91,808,008 / 92.47%
Intronic: 4,544,381 / 4.58%
Intergenic: 2,932,844 / 2.95%
Intronic/intergenic overlapping exon: 4,240,469 / 4.27%

Transcript coverage profile

5' bias: 0.11
3' bias: 0.15
5'-3' bias: 1.86

Junction analysis

Reads at junctions: 29,203,516
ACCT 5.58%
ATCT 4.78%
TCCT 4.76%
AGGT 4.28%
CCCT 2.89%
AGGA 2.8%
GCCT 2.74%
AGGC 2.4%
TCCC 2.34%
AGCT 2%
CGTA 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