Input data and parameters 

Input

Analysis date: Tue Oct 31 09:23:26 GMT 2023
BAM file: SRX7354303.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): 42,000,040 / 41,954,258
Number of aligned pairs (without duplicates): 41,940,916
Total number of alignments: 89,624,275
Number of secondary alignments: 5,669,977
Number of non-unique alignments: 9,610,238
Aligned to genes: 68,407,200
Ambiguous alignments: 188,504
No feature assigned: 11,047,995
Missing chromosome in annotation: 370,338
Not aligned: 6,313,842

Reads genomic origin

Exonic: 68,407,200 / 86.1%
Intronic: 7,050,414 / 8.87%
Intergenic: 3,997,581 / 5.03%
Intronic/intergenic overlapping exon: 3,161,492 / 3.98%

Transcript coverage profile

5' bias: 0.19
3' bias: 0.12
5'-3' bias: 1.76

Junction analysis

Reads at junctions: 18,033,825
ACCT 5.13%
AGGT 4.71%
AGGA 3.84%
ATCT 3.64%
TCCT 3.31%
GCCT 2.89%
AGCT 2.79%
AGAT 2.54%
AGGC 2.35%
CCCT 2.3%
TTCT 2.28%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis