Input data and parameters 

Input

Analysis date: Sun Oct 29 11:42:31 GMT 2023
BAM file: SRX7354094.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): 49,414,447 / 49,365,990
Number of aligned pairs (without duplicates): 49,357,278
Total number of alignments: 105,863,399
Number of secondary alignments: 7,082,962
Number of non-unique alignments: 11,549,153
Aligned to genes: 83,589,758
Ambiguous alignments: 294,154
No feature assigned: 9,814,887
Missing chromosome in annotation: 615,447
Not aligned: 3,301,757

Reads genomic origin

Exonic: 83,589,758 / 89.49%
Intronic: 6,367,889 / 6.82%
Intergenic: 3,446,998 / 3.69%
Intronic/intergenic overlapping exon: 3,446,152 / 3.69%

Transcript coverage profile

5' bias: 0.34
3' bias: 0.23
5'-3' bias: 1.82

Junction analysis

Reads at junctions: 27,428,961
ACCT 5.16%
AGGT 4.61%
TCCT 3.89%
ATCT 3.85%
AGGA 3.36%
GCCT 3.1%
CCCT 2.62%
AGCT 2.61%
AGGC 2.27%
TTCT 2.13%
AGAT 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