Input data and parameters 

Input

Analysis date: Tue Oct 31 09:07:55 GMT 2023
BAM file: SRX7354320.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): 30,429,675 / 30,410,992
Number of aligned pairs (without duplicates): 30,406,980
Total number of alignments: 64,907,002
Number of secondary alignments: 4,066,335
Number of non-unique alignments: 6,801,018
Aligned to genes: 50,778,741
Ambiguous alignments: 169,429
No feature assigned: 6,879,064
Missing chromosome in annotation: 278,750
Not aligned: 2,218,915

Reads genomic origin

Exonic: 50,778,741 / 88.07%
Intronic: 4,870,302 / 8.45%
Intergenic: 2,008,762 / 3.48%
Intronic/intergenic overlapping exon: 1,891,562 / 3.28%

Transcript coverage profile

5' bias: 0.38
3' bias: 0.21
5'-3' bias: 1.94

Junction analysis

Reads at junctions: 17,660,136
ACCT 5.16%
AGGT 4.96%
ATCT 3.77%
AGGA 3.73%
TCCT 3.55%
AGCT 2.84%
GCCT 2.83%
AGGC 2.4%
CCCT 2.3%
AGAT 2.25%
TTCT 2.05%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis