Input data and parameters 

Input

Analysis date: Sun Oct 29 02:07:18 GMT 2023
BAM file: SRX7354091.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): 67,086,173 / 67,016,098
Number of aligned pairs (without duplicates): 67,010,929
Total number of alignments: 143,113,385
Number of secondary alignments: 9,011,114
Number of non-unique alignments: 13,894,813
Aligned to genes: 104,235,314
Ambiguous alignments: 413,812
No feature assigned: 23,480,715
Missing chromosome in annotation: 1,088,731
Not aligned: 5,485,655

Reads genomic origin

Exonic: 104,235,314 / 81.61%
Intronic: 15,407,111 / 12.06%
Intergenic: 8,073,604 / 6.32%
Intronic/intergenic overlapping exon: 5,235,592 / 4.1%

Transcript coverage profile

5' bias: 0.43
3' bias: 0.28
5'-3' bias: 1.65

Junction analysis

Reads at junctions: 44,332,076
ACCT 5.26%
AGGT 4.62%
GCCT 3.71%
TCCT 3.58%
ATCT 3.43%
AGGA 3.41%
CCCT 2.84%
AGCT 2.81%
AGGC 2.48%
AGAT 2.21%
TTCT 2.12%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis