Input data and parameters 

Input

Analysis date: Tue Oct 31 09:25:24 GMT 2023
BAM file: SRX7354302.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): 32,278,872 / 32,243,660
Number of aligned pairs (without duplicates): 32,238,826
Total number of alignments: 68,736,447
Number of secondary alignments: 4,213,915
Number of non-unique alignments: 6,526,165
Aligned to genes: 52,789,240
Ambiguous alignments: 200,624
No feature assigned: 8,679,982
Missing chromosome in annotation: 540,436
Not aligned: 9,622,506

Reads genomic origin

Exonic: 52,789,240 / 85.88%
Intronic: 5,342,589 / 8.69%
Intergenic: 3,337,393 / 5.43%
Intronic/intergenic overlapping exon: 2,264,367 / 3.68%

Transcript coverage profile

5' bias: 0.49
3' bias: 0.29
5'-3' bias: 1.73

Junction analysis

Reads at junctions: 20,024,551
ACCT 5.28%
AGGT 4.65%
GCCT 3.71%
TCCT 3.6%
ATCT 3.51%
AGGA 3.24%
AGCT 2.8%
CCCT 2.7%
AGGC 2.44%
TTCT 2.24%
AGAT 2.03%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis