Input data and parameters 

Input

Analysis date: Tue Oct 31 10:08:41 GMT 2023
BAM file: SRX7354382.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): 53,032,111 / 52,992,423
Number of aligned pairs (without duplicates): 52,970,654
Total number of alignments: 113,957,177
Number of secondary alignments: 7,932,643
Number of non-unique alignments: 13,359,686
Aligned to genes: 89,280,779
Ambiguous alignments: 330,588
No feature assigned: 10,400,524
Missing chromosome in annotation: 585,600
Not aligned: 2,532,034

Reads genomic origin

Exonic: 89,280,779 / 89.57%
Intronic: 6,131,288 / 6.15%
Intergenic: 4,269,236 / 4.28%
Intronic/intergenic overlapping exon: 4,143,351 / 4.16%

Transcript coverage profile

5' bias: 0.39
3' bias: 0.22
5'-3' bias: 1.75

Junction analysis

Reads at junctions: 29,720,911
ACCT 5.54%
AGGT 4.51%
ATCT 3.98%
TCCT 3.87%
GCCT 3.49%
AGGA 3.11%
CCCT 2.79%
AGCT 2.45%
AGGC 2.33%
TTCT 2.2%
AGGG 1.75%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis