Input data and parameters 

Input

Analysis date: Tue Oct 31 09:57:01 GMT 2023
BAM file: SRX7354407.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): 52,372,451 / 52,318,207
Number of aligned pairs (without duplicates): 52,310,149
Total number of alignments: 111,082,708
Number of secondary alignments: 6,392,050
Number of non-unique alignments: 10,618,652
Aligned to genes: 87,946,642
Ambiguous alignments: 342,128
No feature assigned: 11,752,448
Missing chromosome in annotation: 422,838
Not aligned: 8,777,822

Reads genomic origin

Exonic: 87,946,642 / 88.21%
Intronic: 8,038,926 / 8.06%
Intergenic: 3,713,522 / 3.72%
Intronic/intergenic overlapping exon: 3,548,548 / 3.56%

Transcript coverage profile

5' bias: 0.33
3' bias: 0.18
5'-3' bias: 1.88

Junction analysis

Reads at junctions: 31,453,401
ACCT 5.34%
AGGT 4.74%
AGGA 3.58%
ATCT 3.52%
TCCT 3.39%
GCCT 3.05%
AGCT 2.78%
AGGC 2.39%
CCCT 2.3%
AGAT 2.26%
TTCT 2.19%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis