Input data and parameters 

Input

Analysis date: Mon Oct 30 11:08:00 GMT 2023
BAM file: SRX7354169.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): 35,480,002 / 35,455,077
Number of aligned pairs (without duplicates): 35,451,305
Total number of alignments: 75,229,006
Number of secondary alignments: 4,293,927
Number of non-unique alignments: 7,234,305
Aligned to genes: 58,191,198
Ambiguous alignments: 190,978
No feature assigned: 9,319,653
Missing chromosome in annotation: 292,872
Not aligned: 7,300,127

Reads genomic origin

Exonic: 58,191,198 / 86.2%
Intronic: 5,833,759 / 8.64%
Intergenic: 3,485,894 / 5.16%
Intronic/intergenic overlapping exon: 2,390,007 / 3.54%

Transcript coverage profile

5' bias: 0.26
3' bias: 0.14
5'-3' bias: 2.33

Junction analysis

Reads at junctions: 16,390,684
ACCT 5.48%
AGGT 4.73%
ATCT 3.65%
AGGA 3.59%
TCCT 3.42%
GCCT 3.09%
AGCT 2.75%
AGGC 2.38%
AGAT 2.34%
CCCT 2.31%
TTCT 2.22%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis