Input data and parameters 

Input

Analysis date: Mon Oct 30 20:23:17 GMT 2023
BAM file: SRX7354220.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): 42,567,660 / 42,543,232
Number of aligned pairs (without duplicates): 42,539,468
Total number of alignments: 90,586,765
Number of secondary alignments: 5,475,873
Number of non-unique alignments: 9,205,517
Aligned to genes: 72,381,119
Ambiguous alignments: 274,588
No feature assigned: 8,395,995
Missing chromosome in annotation: 329,546
Not aligned: 3,313,272

Reads genomic origin

Exonic: 72,381,119 / 89.61%
Intronic: 5,539,913 / 6.86%
Intergenic: 2,856,082 / 3.54%
Intronic/intergenic overlapping exon: 2,523,726 / 3.12%

Transcript coverage profile

5' bias: 0.35
3' bias: 0.21
5'-3' bias: 1.9

Junction analysis

Reads at junctions: 24,057,603
ACCT 5.28%
AGGT 4.62%
ATCT 3.62%
AGGA 3.51%
TCCT 3.49%
GCCT 3.12%
AGCT 2.75%
AGGC 2.44%
CCCT 2.42%
AGAT 2.23%
TTCT 2.23%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis