Input data and parameters 

Input

Analysis date: Sun Oct 29 12:48:09 GMT 2023
BAM file: SRX7354141.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): 52,098,285 / 52,057,654
Number of aligned pairs (without duplicates): 52,052,614
Total number of alignments: 110,898,944
Number of secondary alignments: 6,743,005
Number of non-unique alignments: 11,284,100
Aligned to genes: 84,459,474
Ambiguous alignments: 316,399
No feature assigned: 14,418,226
Missing chromosome in annotation: 420,745
Not aligned: 3,401,383

Reads genomic origin

Exonic: 84,459,474 / 85.42%
Intronic: 10,142,194 / 10.26%
Intergenic: 4,276,032 / 4.32%
Intronic/intergenic overlapping exon: 3,363,176 / 3.4%

Transcript coverage profile

5' bias: 0.39
3' bias: 0.22
5'-3' bias: 1.83

Junction analysis

Reads at junctions: 27,875,792
ACCT 5.37%
AGGT 4.7%
AGGA 3.55%
ATCT 3.48%
TCCT 3.43%
GCCT 3.18%
AGCT 2.75%
CCCT 2.45%
AGGC 2.4%
AGAT 2.32%
TTCT 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