Input data and parameters 

Input

Analysis date: Tue Oct 31 09:32:03 GMT 2023
BAM file: SRX7354314.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): 44,621,804 / 44,541,931
Number of aligned pairs (without duplicates): 44,519,442
Total number of alignments: 96,286,785
Number of secondary alignments: 7,123,050
Number of non-unique alignments: 11,214,189
Aligned to genes: 76,533,741
Ambiguous alignments: 332,960
No feature assigned: 7,527,045
Missing chromosome in annotation: 678,850
Not aligned: 5,872,927

Reads genomic origin

Exonic: 76,533,741 / 91.05%
Intronic: 4,131,599 / 4.92%
Intergenic: 3,395,446 / 4.04%
Intronic/intergenic overlapping exon: 3,147,267 / 3.74%

Transcript coverage profile

5' bias: 0.1
3' bias: 0.14
5'-3' bias: 1.77

Junction analysis

Reads at junctions: 22,147,650
TCCT 5.27%
ACCT 5.09%
ATCT 4.57%
AGGT 4.19%
CCCT 3.49%
AGGA 2.83%
GCCT 2.39%
AGGC 2.37%
TTCT 2.1%
AGCT 2.05%
AGAC 1.92%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis