Input data and parameters 

Input

Analysis date: Mon Oct 30 20:29:47 GMT 2023
BAM file: SRX7354175.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): 41,245,765 / 41,226,929
Number of aligned pairs (without duplicates): 41,189,898
Total number of alignments: 88,665,895
Number of secondary alignments: 6,193,201
Number of non-unique alignments: 10,000,213
Aligned to genes: 70,358,603
Ambiguous alignments: 280,250
No feature assigned: 7,468,405
Missing chromosome in annotation: 558,424
Not aligned: 1,322,076

Reads genomic origin

Exonic: 70,358,603 / 90.4%
Intronic: 4,320,180 / 5.55%
Intergenic: 3,148,225 / 4.05%
Intronic/intergenic overlapping exon: 3,529,453 / 4.53%

Transcript coverage profile

5' bias: 0.21
3' bias: 0.16
5'-3' bias: 2.72

Junction analysis

Reads at junctions: 23,143,007
ACCT 5.33%
TCCT 5.18%
ATCT 4.7%
AGGT 4.17%
CCCT 3.2%
GCCT 3.14%
AGGA 2.77%
TTCT 2.37%
AGGC 2.22%
TCCC 2.16%
AGCT 2.15%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis