Input data and parameters 

Input

Analysis date: Sun Oct 29 12:19:54 GMT 2023
BAM file: SRX7354061.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): 44,847,581 / 44,822,597
Number of aligned pairs (without duplicates): 44,813,520
Total number of alignments: 96,368,813
Number of secondary alignments: 6,698,635
Number of non-unique alignments: 10,701,358
Aligned to genes: 76,980,781
Ambiguous alignments: 307,655
No feature assigned: 7,756,371
Missing chromosome in annotation: 622,648
Not aligned: 3,137,260

Reads genomic origin

Exonic: 76,980,781 / 90.85%
Intronic: 4,954,938 / 5.85%
Intergenic: 2,801,433 / 3.31%
Intronic/intergenic overlapping exon: 3,403,529 / 4.02%

Transcript coverage profile

5' bias: 0.15
3' bias: 0.15
5'-3' bias: 1.76

Junction analysis

Reads at junctions: 23,887,359
ACCT 5.23%
TCCT 4.86%
AGGT 4.53%
ATCT 4.31%
AGGA 3.23%
CCCT 2.96%
GCCT 2.64%
AGGC 2.2%
TTCT 2.19%
AGCT 2.13%
AGAA 1.89%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis