Input data and parameters 

Input

Analysis date: Sun Oct 29 01:55:51 GMT 2023
BAM file: SRX7354150.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): 40,803,528 / 40,757,692
Number of aligned pairs (without duplicates): 40,701,477
Total number of alignments: 89,415,847
Number of secondary alignments: 7,854,627
Number of non-unique alignments: 10,636,133
Aligned to genes: 68,665,649
Ambiguous alignments: 287,450
No feature assigned: 8,095,545
Missing chromosome in annotation: 1,731,070
Not aligned: 4,250,922

Reads genomic origin

Exonic: 68,665,649 / 89.45%
Intronic: 4,273,332 / 5.57%
Intergenic: 3,822,213 / 4.98%
Intronic/intergenic overlapping exon: 3,365,273 / 4.38%

Transcript coverage profile

5' bias: 0.24
3' bias: 0.2
5'-3' bias: 1.96

Junction analysis

Reads at junctions: 21,279,171
ACCT 5.39%
TCCT 4.49%
AGGT 4.41%
ATCT 4.38%
GCCT 3.53%
AGGA 2.98%
CCCT 2.91%
TTCT 2.3%
AGCT 2.23%
AGGC 2.23%
TCCC 1.75%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis