Input data and parameters 

Input

Analysis date: Mon Oct 30 23:00:54 GMT 2023
BAM file: SRX7354286.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): 50,804,449 / 50,767,969
Number of aligned pairs (without duplicates): 50,749,427
Total number of alignments: 110,041,040
Number of secondary alignments: 8,468,622
Number of non-unique alignments: 13,310,122
Aligned to genes: 87,019,877
Ambiguous alignments: 300,344
No feature assigned: 8,473,427
Missing chromosome in annotation: 937,270
Not aligned: 4,721,272

Reads genomic origin

Exonic: 87,019,877 / 91.13%
Intronic: 4,601,633 / 4.82%
Intergenic: 3,871,794 / 4.05%
Intronic/intergenic overlapping exon: 3,835,860 / 4.02%

Transcript coverage profile

5' bias: 0.1
3' bias: 0.13
5'-3' bias: 1.89

Junction analysis

Reads at junctions: 25,639,743
ACCT 5.65%
TCCT 4.87%
ATCT 4.76%
AGGT 4.1%
CCCT 3.14%
GCCT 2.86%
AGGA 2.83%
TCCC 2.5%
AGGC 2.21%
CGTA 2.07%
CCCA 1.98%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis