Input data and parameters 

Input

Analysis date: Mon Oct 30 13:03:09 GMT 2023
BAM file: SRX7354208.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): 56,228,801 / 56,155,407
Number of aligned pairs (without duplicates): 56,130,702
Total number of alignments: 120,547,792
Number of secondary alignments: 8,163,584
Number of non-unique alignments: 12,342,100
Aligned to genes: 92,451,525
Ambiguous alignments: 371,631
No feature assigned: 14,209,486
Missing chromosome in annotation: 1,173,050
Not aligned: 2,411,982

Reads genomic origin

Exonic: 92,451,525 / 86.68%
Intronic: 10,235,938 / 9.6%
Intergenic: 3,973,548 / 3.73%
Intronic/intergenic overlapping exon: 4,896,593 / 4.59%

Transcript coverage profile

5' bias: 0.49
3' bias: 0.24
5'-3' bias: 1.73

Junction analysis

Reads at junctions: 35,158,914
ACCT 5.27%
AGGT 4.7%
ATCT 3.7%
TCCT 3.42%
AGGA 3.36%
GCCT 3.33%
CCCT 2.83%
AGCT 2.7%
AGGC 2.42%
TTCT 2.16%
AGAT 2.07%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis