Input data and parameters 

Input

Analysis date: Tue Oct 31 09:31:07 GMT 2023
BAM file: SRX7354245.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): 41,221,056 / 41,195,930
Number of aligned pairs (without duplicates): 41,192,887
Total number of alignments: 88,541,497
Number of secondary alignments: 6,124,511
Number of non-unique alignments: 9,880,692
Aligned to genes: 69,580,110
Ambiguous alignments: 224,208
No feature assigned: 8,230,866
Missing chromosome in annotation: 625,621
Not aligned: 2,354,474

Reads genomic origin

Exonic: 69,580,110 / 89.42%
Intronic: 5,015,738 / 6.45%
Intergenic: 3,215,128 / 4.13%
Intronic/intergenic overlapping exon: 2,511,066 / 3.23%

Transcript coverage profile

5' bias: 0.41
3' bias: 0.22
5'-3' bias: 1.81

Junction analysis

Reads at junctions: 20,845,453
ACCT 5.34%
AGGT 4.7%
ATCT 3.71%
AGGA 3.52%
TCCT 3.41%
GCCT 3.25%
AGCT 2.8%
CCCT 2.65%
AGGC 2.36%
TTCT 2.27%
AGAT 2.2%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis