Input data and parameters 

Input

Analysis date: Mon Oct 30 13:20:06 GMT 2023
BAM file: SRX7354209.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): 78,289,305 / 78,247,946
Number of aligned pairs (without duplicates): 78,238,085
Total number of alignments: 167,937,749
Number of secondary alignments: 11,400,498
Number of non-unique alignments: 17,325,739
Aligned to genes: 136,880,191
Ambiguous alignments: 577,767
No feature assigned: 11,674,113
Missing chromosome in annotation: 1,479,939
Not aligned: 4,940,945

Reads genomic origin

Exonic: 136,880,191 / 92.14%
Intronic: 6,782,564 / 4.57%
Intergenic: 4,891,549 / 3.29%
Intronic/intergenic overlapping exon: 5,312,687 / 3.58%

Transcript coverage profile

5' bias: 0.12
3' bias: 0.17
5'-3' bias: 1.47

Junction analysis

Reads at junctions: 47,474,137
ACCT 5.22%
AGGT 4.8%
TCCT 4.05%
ATCT 4.01%
CCCT 3.22%
AGGA 3.1%
AGGC 2.58%
GCCT 2.53%
AGCT 2.12%
TTCT 2.06%
AGAA 1.97%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis