Input data and parameters 

Input

Analysis date: Tue Oct 31 11:45:53 GMT 2023
BAM file: SRX7354406.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): 35,646,823 / 35,628,472
Number of aligned pairs (without duplicates): 35,625,729
Total number of alignments: 76,108,967
Number of secondary alignments: 4,833,672
Number of non-unique alignments: 8,082,847
Aligned to genes: 60,179,478
Ambiguous alignments: 201,343
No feature assigned: 7,285,622
Missing chromosome in annotation: 359,677
Not aligned: 3,358,803

Reads genomic origin

Exonic: 60,179,478 / 89.2%
Intronic: 4,591,958 / 6.81%
Intergenic: 2,693,664 / 3.99%
Intronic/intergenic overlapping exon: 2,019,412 / 2.99%

Transcript coverage profile

5' bias: 0.36
3' bias: 0.18
5'-3' bias: 2.19

Junction analysis

Reads at junctions: 19,150,496
ACCT 5.45%
AGGT 4.69%
AGGA 3.57%
ATCT 3.55%
TCCT 3.45%
GCCT 3.24%
AGCT 2.7%
CCCT 2.39%
AGAT 2.36%
AGGC 2.35%
TTCT 2.16%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis