Input data and parameters 

Input

Analysis date: Sun Oct 29 12:33:38 GMT 2023
BAM file: SRX7354145.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): 42,978,960 / 42,957,840
Number of aligned pairs (without duplicates): 42,950,386
Total number of alignments: 92,496,504
Number of secondary alignments: 6,559,704
Number of non-unique alignments: 9,876,622
Aligned to genes: 74,257,857
Ambiguous alignments: 284,308
No feature assigned: 7,137,539
Missing chromosome in annotation: 940,178
Not aligned: 2,070,928

Reads genomic origin

Exonic: 74,257,857 / 91.23%
Intronic: 4,317,226 / 5.3%
Intergenic: 2,820,313 / 3.46%
Intronic/intergenic overlapping exon: 2,811,043 / 3.45%

Transcript coverage profile

5' bias: 0.23
3' bias: 0.19
5'-3' bias: 2.09

Junction analysis

Reads at junctions: 21,278,777
ACCT 5.1%
AGGT 4.93%
TCCT 4.02%
ATCT 3.88%
AGGA 3.51%
CCCT 2.84%
GCCT 2.69%
AGCT 2.43%
AGGC 2.34%
TTCT 2.18%
AGAA 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