Input data and parameters 

Input

Analysis date: Sun Oct 29 12:26:57 GMT 2023
BAM file: SRX7354158.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): 38,040,597 / 38,020,033
Number of aligned pairs (without duplicates): 38,017,133
Total number of alignments: 80,835,963
Number of secondary alignments: 4,775,333
Number of non-unique alignments: 8,054,755
Aligned to genes: 63,604,908
Ambiguous alignments: 213,872
No feature assigned: 8,703,730
Missing chromosome in annotation: 258,698
Not aligned: 3,390,404

Reads genomic origin

Exonic: 63,604,908 / 87.96%
Intronic: 6,062,516 / 8.38%
Intergenic: 2,641,214 / 3.65%
Intronic/intergenic overlapping exon: 2,260,038 / 3.13%

Transcript coverage profile

5' bias: 0.37
3' bias: 0.17
5'-3' bias: 1.97

Junction analysis

Reads at junctions: 21,012,666
ACCT 5.62%
AGGT 4.67%
ATCT 3.63%
AGGA 3.55%
TCCT 3.42%
GCCT 3.39%
AGCT 2.74%
AGGC 2.38%
CCCT 2.36%
AGAT 2.29%
TTCT 2.16%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis