Input data and parameters 

Input

Analysis date: Sun Oct 29 01:20:47 GMT 2023
BAM file: SRX7354146.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): 41,826,372 / 41,785,163
Number of aligned pairs (without duplicates): 41,758,058
Total number of alignments: 89,989,708
Number of secondary alignments: 6,378,173
Number of non-unique alignments: 10,190,399
Aligned to genes: 68,429,947
Ambiguous alignments: 312,558
No feature assigned: 10,549,570
Missing chromosome in annotation: 507,234
Not aligned: 1,498,271

Reads genomic origin

Exonic: 68,429,947 / 86.64%
Intronic: 8,381,224 / 10.61%
Intergenic: 2,168,346 / 2.75%
Intronic/intergenic overlapping exon: 3,736,947 / 4.73%

Transcript coverage profile

5' bias: 0.42
3' bias: 0.23
5'-3' bias: 1.84

Junction analysis

Reads at junctions: 29,140,470
ACCT 5.28%
AGGT 4.68%
TCCT 3.64%
AGGA 3.49%
ATCT 3.37%
GCCT 3%
AGCT 2.74%
CCCT 2.57%
AGGC 2.52%
AGGG 2.04%
AGAT 2.04%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis